Lilly's Story: The Indigo Chapter Part 1
by Lord-Saxon13
Summary: After finding a Spiky Eared Pichu, Ash ends up being the target of the villain known The Collector and his hired help Isabella Black. Ash will journey across Kanto finding the pichu's story. In the process tangling with Professor Technology and The Techno Institute, Team Nature, the mysterious Doctor Order and The Chairman. NOT BEING UPDATED ANYMORE REMAKE OUT NOW.
1. Meeting The Pichu

**Do not own Pokémon**

 **UPDATE:**

 **Story Changes + Additions / Spelling and Grammar Checked**

 **Renamed from The Story Begins to Meeting The Pichu**

 **UPDATE 2 [08/09/2017]:**

 **More Spelling and Grammar Fixed**

 **Lilly's Story: The Indigo Chapter Part 1**

 **Chapter 1: Meeting The Pichu**

A female in a hooded cloak was running from The Collector, a Pokémon hunter that wanted to collect rare Pokémon for his private collection and who used stolen advanced technology to advance his aims. She was holding a small Pokémon in her hands that The Collector was after. She made to a fork in the path and said to the small Pokémon "Go right and I will lead them away" The small Pokémon nodded and went right. The female in the hooded cloak made sure that The Collector saw her go left.

Nearby on a TV, a news reporter was saying "The insane super villain Doctor Order is still at large. The Techno Institute has issued a warning stating do not approach if she spotted. They consider her to be armed and dangerous" This is being watched by a ten years old boy from Pallet Town named Ash Ketchum. He is sitting on the sofa in his living room. Ash Ketchum has raven hair and brown eyes. Ash was wearing PJs. "Unfortunately, no photos are available as we have no idea of her real identity. In other news, a new factory built by Nuclear Industries has been targeted by an eco-terrorist group calling themselves Team Nature"

Ash's mother, Delia Ketchum then entered the room. Delia looked at a clock and then said frowning "it's well past your bedtime"

Ash said "But Mom…. I'm too excited to go asleep" referring to the fact he can pick his starter Pokémon the next day.

Delia said not budging "It's time for bed. It's nearly 11 o'clock at night and you should be asleep" Ash looked at his mother and went upstairs to his bedroom.

Meanwhile near Pallet Town, a man with short white hair and blue eyes wearing a black suit and black glasses with black tinted lenses was overseeing his crew of people dressed in black with a green N on their chests lifting an ancient coffin out of an unmarked grave. He said to the crew "We have done it, our mistress has been found, now we will emerge from the shadows to destroy technology"

Ash awoke the next morning to find it to be late morning and that his Voltorb-shaped alarm clock broken against the wall next to his bed. He was so afraid that he had overslept so he ran out of the house in just his PJs. He bolted to Professor Oak's Laboratory across town. Outside the laboratory, a crowd of people has gathered, including a group of cheerleaders. Ash then made it to the lab to see his rival, the professor's grandson, Gary Oak.

He was the same age as Ash; he had brown hair and black eyes. Gary taunted Ash and said, "Late again Ketchum, I already have received my starter Pokémon from my grandfather" Gary then spoke to the crowd and said, "I will make Pallet Town famous by becoming a Pokémon Master" The crowd cheered" Gary not waiting for a response so left in a red sports car. The crowd followed and broke up.

Ash entered the lab catching a radio saying "…. experts studying weather patterns have noticed a rise of strange weather all over Kanto. Some experts have noted that it is like the weather patterns that occurred just before The Super Storm hit a decade ago"

Inside Oak's laboratory, three Poké Balls were set up on a storage device, with a place for a fourth in the center. The rest of the lab was a mess. Professor Oak was nowhere to be seen. Ash decides that he would like to start with Squirtle, but when he opens the Poké Ball, he finds that it is empty. After this, Ash decides he would like Bulbasaur, but this Poké Ball is also empty. He has no choice but to go for the last choice, Charmander, but the final Poké Ball is also empty. Professor Oak arrived from the back room with a sad look on his face. "I sorry Ash, but they all gone"

Ash asked remembering about a Pokémon he saw when was little and was playing in Oak's garden "What about the other Pokémon you have professor?"

Professor Oak lies not wanting Ash to have the Pokémon that he believed wasn't ready for a trainer "Oh that one is already taken" before saying "maybe next year" Oak watched as Ash left the lab looking sad.

Ash walked away from the lab looking sad when he saw something out of the corner of his eye. He found himself on edge of the woods surrounding Pallet Town facing a strange old oak tree that was glowing purple that Ash did not believe was there before. He walked forwards towards the tree. He approached the strange old oak tree that hummed with a strange energy. As he neared the tree, a Spiky-eared Pichu poked its head out. Ash said gently "Hello" The Pichu looked at him with interest. Ash sat on the ground and beckoned the Pichu to come over. The Pichu slowly went over to him and nuzzled his hand. Ash smiled.

He sat there peacefully for a while with the Pichu licking his hand when a robotic voice said, "Found you" Ash looked to see a kid wearing strange goggles on a strange flying machine backed up by a gang of Spearow. The kid said, "give me the Pichu"

Ash said determined, working out that this kid was bad news "No"

"You dare say no to me, I am The Collector," said The Collector. He pressed a few buttons on his flying machine. A Spearow swoops down at Ash. Ash rolled out of the way. The Spearow knocked itself out. The Collector looked angry and pressed more buttons. Ash carrying the Pichu started to run as The Spearow Flock started flying towards him. They were followed by The Collector. As Ash runs, the Pichu sends out sparks in fear. Ash tries to lose them in the forest but The Collector and his Spearow kept coming. Ash not paying attention to what's in front of him falls in the river and falls down a waterfall into a large pond. Ash climbs out the water to find a few feet away, a crazy looking girl with white hair sitting on the ground creepy staring at nothing with emotionless eyes.

Ash said "Hello" but the girl did not respond. At that moment, Ash hears the distant cries of Spearow and makes a run for it. The girl did not move even as the flock of Spearow knocked her over. Ash heads towards Viridian City, with the flock of Spearow in close pursuit. Ash trips and finds face flat on the ground.

Ash finds himself looking at the trembling Pichu as The Collector's voice said impatiently "Hand me the Pichu now" He waited a moment before saying "get him" With the Spearow approaching Ash grew hopeless. Looking at the pleading eyes of the Pichu, Ash brings them to his chest. However, just as the Spearow are diving upon Ash, the Pichu glows purple and they slow down and a blast of purple lighting takes out the entire flock of Spearow, as well as hitting The Collector. The Collector's machine exploded causing him to go flying. The Collector said, "You haven't seen the last of me" as he blasted off. Ash sees this and stroked the tried Pichu grateful of her strange power which saved him. Ash puts The Pichu on his shoulder. Drained the Pichu wrapped herself around Ash's neck. Ash rises from the ground, exhausted but victorious. He starts making his way to Viridian City to get her checked out.

Inside Tech Manor was its owner, Professor Technology, an elderly man in a lab coat with a logo of a black factory with a white T on his front pocket talking with holograms of The Board of Executives led by Chairman von Nuclear. He was both Chairman of Nuclear Industries and Chief Executive of The Techno Institute. Chairman von Nuclear was a handsome man in an expensive suit. Professor Technology was saying "Gentlemen, Project M2 is entering its final stages and soon nothing can stop us"

Chairman von Nuclear said "Professor, The Board and I are concerned over the fact Doctor Order is still at large and now this eco terrorist group, Team Nature has surfaced. On top of this, some of our advanced technology in your hands was stolen from under your nose by some spoiled brat. We have backed this project as you assured us that Doctor Order would be dealt with within a year. That was five years ago now and you still haven't made progress. We need results or The Board will be forced to replace you"

Professor Technology said in response "All I need is more time"

Chairman von Nuclear said "As a sign of our friendship, you will have 2 more weeks, the meeting is adjourned" The Board of Executives then vanished. Professor Technology smirked to himself as soon he will have no need for The Board of Executives so was unconcerned with their threat.


	2. Lilly and Eve

**Do not own Pokémon**

 **Each chapter is based around an Episode of the anime.**

 _ **UPDATE: Story Changes + Additions / Spelling and Grammar Checked**_

 _ **Renamed from Techno Attacks to Lilly and Eve**_

 **Lilly's Story: The Indigo League**

 **Chapter 2:** **Lilly and Eve**

On the orbiting Techno Institute space station known as Zeus, a Captain Zed caught the reading of the purple lighting. He smirked and pressed a button activating one of their agents, The Techno Samurai to hunt the source.

Ash was making his way to Viridian City, carrying an exhausted pichu on one shoulder. He has decided to head to the Viridian City Pokémon Centre to get her checked over and contract Professor Oak on what do with the pichu. On his way into town, trucks with carrying men in hunting gear blasted past. As Ash enters the town, he is stopped by a woman wearing Police uniform and who was on a motorbike. Ash asked "Yes Officer?"

The police woman who was called Officer Jenny said suspiciously "Why is that Pichu not in a Poké Ball? And who are you?"

Ash said "I'm Ash Ketchum. Well the fact is I do not know if this Pokémon has one. I saved her from a guy calling himself The Collector and was on my way to contract Professor Oak"

Officer Jenny said "In that case I get you to a Pokémon Centre as he is no doubt in the area" Ash nodded in thanks and climbed on. Officer Jenny drove off and headed to the Pokémon Centre on her motorbike He doesn't notice the white-haired girl emerge from the trees following the bike.

Up in the sky, The Collector in a new flying machine pulls out a tablet and pressed a few buttons. He mutters to himself "let's see what this toy does". He throws a Poké Ball into a dark alley. A Mecha-Meowth, a robot version of a Meowth crawled out. It then stood up straight and was the size of the buildings of the alley. "This more like it" The Collector said as he messed with the tablet. This made Mecha-Meowth stomp off in the direction of the Pokémon Centre. The Collector followed.

Ash was dropped off at the Pokémon Centre. He thanks Officer Jenny and carries Lilly into the centre. Office Jenny was saying into a walkie-talkie "The Collector has been sighted in the area"

Ash went over to a woman wearing a nurse uniform and She said "I'm Nurse Joy, what's wrong?"

Ash told her "I want you to check over this pichu, we were attacked by The Collector" Nurse Joy nodded and put the pichu on a stretcher. A Chansey took the stretcher away. He asked in a voice full of worry "How do I call home?"

Nurse Joy said "The video screens over there" She pointed to an empty one. Ash went over to it and called Professor Oak. Professor Oak appeared on the screen looking surprised.

Professor Oak inquired "What are you doing in Viridian?" Ash told him, story of meeting the pichu and The Collector. Professor Oak said in response "The pichu must be special if The Collector is personally hunting it down, I want you to stay with the pichu for the moment" Ash nodded in response "I inform your mother on this so she doesn't worry. I wish you luck on this but I'm afraid I must go now. I will try to meet with you soon" He then hanged up and the screen went back. Ash was about to go over to Nurse Joy but at that moment, the white-haired girl entered the Pokémon Centre and came over him.

The girl said emotionless voice "Hello"

Ash said find the girl slightly unsettling "Hello again"

The girl said "Sorry for not answering you earlier, my mind was miles away. you can call me Eve"

Ash said with nothing else to say "I'm Ash Ketchum"

Eve said "what happened to The Pichu that you were with"

Ash said "getting checked over" just as Nurse Joy the pichu back.

Eve asked "what's her name?"

Ash said "she doesn't have one as far as I know"

Eve said "that won't do…." she thought for a moment "Lilly's a nice name isn't it little one" Lilly smiled in response. Ash jumped when Mecha-Meowth came crashing through the opposite wall.

The Collector flew in after it, he saw Ash and demanded "Give the pichu or my new friend will crush you" At Eve's urging, Ash releases a Pidgey and a Rattata from Poké Balls that have been knocked to the floor, but they are whacked aside by Mecha-Meowth. "You can't defeat me that easily this time" Ash and Eve then flee and are chased down a corridor by Mecha-Meowth and The Collector. Nurse Joy and the people inside the centre take this chance to flee out of front door. Ash and Eve run down a dead-end corridor. The Collector exclaimed "I got you now" Mecha-Meowth advanced. "nothing can save you" The Mecha-Meowth suddenly stops dead. The Collector muttered to himself "no wonder this was the bin" He manically pressed a load of buttons so did not notice The Mecha-Meowth start shaking. Ash grabs Eve and bolts for it. They make it out as the Pokémon Centre is destroyed by an explosion. Officer Jenny arrived too late to do anything except watch the explosion unfold and The Collector once again go flying. Eve dragged Ash towards Viridian Forest just as Techno Policemen arrived.

Somewhere in Viridian Forest was Zana, a female trainer from Pallet Town, making her way through the forest. She was annoyed as she had been nearly run over by the trucks with carrying men in hunting gear. She paused when she saw a robot that looked like a walking suit of white hi-tech samurai with a logo of a black factory with a white T on the helmet crashing through the trees. It spotted her so she ran for it. The Techno Samurai chased her.

The female in hooded cloak had realized to late that The Collector wasn't the one tracking her when she was confronted by The Collector's hired mercenary known only by her alias, Isabella Black. The female in hooded cloak was worried unlike The Collector who was mostly harmless despite him claiming otherwise, Isabella was a ruthless and convicted killer who cared only for money. Isabella smirked as she trapped the female in hooded cloak on edge of cliff. Isabella said menacingly "Give me The Pichu"

The female in hooded cloak snorted and said "you can see I don't have her anymore"

Isabella said rather calm "Then fortunately for you, The Collector is only paying for the pichu. See you soon princess" She then summersaulted over the female in hooded cloak much to her surprise. She watched in horror as Isabella fell over the cliff. She peered down to see Isabella on the ground unharmed. Isabella winked at her and vanished into the surrounding trees of Viridian Forest.


	3. The Hunters of Viridian Forest Part I

**Do not own Pokémon**

 **Each chapter is based around an Episode of the anime.**

 _ **UPDATE: Story Changes + Additions / Spelling and Grammar Checked**_

 _ **Renamed from Viridian Forest Part I**_ _**to The Hunters of Viridian Forest Part I**_

 **Lilly's Story: The Indigo League**

 **Chapter 3: The Hunters of Viridian Forest Part I**

The nervous trainer named Gerald who was also from Pallet Town was slowly making his way through Viridian Forest. He was jumping at every sound he heard. He was still surprised by the looming figure of The Techno Samurai. He was caught in a net and The Techno Samurai dragged him off.

Eve dragged Ash into Viridian Forest. Eve then stopped in a clearing and let go of Ash. Ash questioned "What was that for?"

Eve just said "We are here so I can teach you how to be a Pokémon trainer, I see great potential in you to do well. in fact, one day you may be able to take on the great Doctor Order in battle"

Ash asked "Why are you doing this?"

Eve said "For Lilly of course, you been lucky so far that you only tangled with The Collector, the lamest of all villains. There are lot more powerful villains out there" Eve then indicated a wild Caterpie. She handed him a Poké Ball from her pocket. "The first step in your training is catch the Caterpie" Ash threw a Poké Ball at a wild Caterpie. As the device pulls Caterpie inside Ash, Eve and Lilly watch as Caterpie tries to break out. Caterpie fails to escape and Lilly smiles at Ash success at getting Caterpie. Eve said "Well done but try to remember next time to weaken the Pokémon before catching it" Ash then decides to bring Caterpie out. Lilly waved to Caterpie. Caterpie gave a small smile.

Ash said "Caterpie crawl up onto my shoulder" Caterpie complied. Lilly snuggled against Caterpie and Ash was happy that they were friends already.

Eve said "Excellent work, you are a natural in this"

They then freeze when they hear The Collector say "Guess who"

Eve said joking "Mr. Lame?" as they turned to see The Collector on yet another flying machine

The Collector said in anger "I'm not lame" slamming his hand on the controls of his machine causing it to explode. "I be back" he screamed as he went flying.

Eve said "See useless villain" and led Ash to an old tree stump. She said "It's getting late now so let's set up camp and start lesson 2 in the morning" Ash sets up the camp near where Eve started a fire. Eve pulled out a large, advanced black wristwatch with the Silph Co logo on it when they had finished "Here take this Pokégear-Zero, the prototype of the Pokémon Gear or Pokégear"

Ash exclaimed "Where did you get this?"

Eve said "I acquired it when I was working for The Techno Institute. I helped create it so I took it when I was unfairly fired" She handed it to him. "Just in case I need to contract you at any point. Goodnight Ash" Eve laid in her sleeping bag and intermediately fell asleep. Ash got into a sleeping bag given to him by Eve, Ash then put the watch on and fell asleep. During the night, Ash thinks he dreams of being awoken by Lilly to see a wonderful starlight view. He gasped at how beautiful it was and said "Thanks guys"

Ash saw Caterpie looking up to the moon with a look on his face as Lilly said "Caterpie has a strong desire to fly as a fully evolved Butterfree. You help him right"

Ash stroked Caterpie and said "I will Caterpie" Caterpie smiled at this and curled up and went to sleep.

Back in Viridian City, the abandoned Viridian Gym was a meeting between the hologram Chairman von Nuclear with a member of The Board, a cruel blue haired man named Damian. He was saying "Chairman, today The Collector tried using one of our inventions and looking at the footage, we can see Project L"

Chairman von Nuclear said "excellent work, the reading recording by Captain Zed must have been her"

Damian asked "What do we do now Chairman?"

Chairman von Nuclear said "nothing for the moment, Professor Technology still has two weeks. My hands are tied by the rest of the board. So, for the moment, we must wait"

The next day, Ash awoke to find Eve creepily staring at nothing again. Ash said "Morning"

It took a moment before Eve said "Morning" back. She shook her before standing up. When Ash was ready she said "Come". Ash follows and Eve said "Catch the Pidgey" pointing to a Pidgey sitting near a brush. Ash threw a Poké Ball but Pidgey simply swats it away. Pidgey posed itself for battle. Eve reminded him "Remember you need to weaken most Pokémon before you can catch them" Ash to summons Caterpie to battle the Caterpie. Caterpie tried to attack but Pidgey was too strong and it sends Caterpie spiraling into a tree. "Lesson 2, Caterpie is at a type disadvantage against Pidgey which means Caterpie is at disadvantage. While type disadvantage is important, the stronger Pokémon can win even it is at a type disadvantage" Pidgey attempts to swoop in for another attack. Eve suggests calmly "Recall Caterpie" and Ash recalls Caterpie to its Poké Ball just moments before Pidgey could strike. Pidgey instead gets its beak lodged into the tree.

Ash says with no other option "Lilly go for it" Lilly jumps in determined just as Pidgey frees itself. Pidgey's attacks but Lilly expertly dodges. Ash says not knowing what moves Lily knows "Attack" Lilly uses Disarming Voice which causes Pidgey to pause to deal with emotional damage. Ash took the chance to toss a Poké Ball. The Ball takes Pidgey in and drops to the ground. It starts rocking. After a few moments, the Ball ceases movement; Ash has captured the Pidgey. Ash was proud. Lilly climbs back onto Ash's shoulder.

Eve said "Well Done Lesson 2 complete" as The Collector reappears in the sky.

The Collector said "I'm back and this time, I will…" They hear gun shots and a swarm of scared Pidgey knock The Collector out of his flying machine and on to the ground. two men hunting gear came running through the trees. They stop when they see The Collector, Eve and Ash.

The first Poacher said "Well look here boys we have some punk kids" The Poachers advanced on the three of them.

The second Poacher said "Whatever Let's just attack" They then send out a Koffing and Ekans to battle. Lilly then jumps down. The Collector released an Unown C.

The first Poacher ordered "Sludge" Koffing's Sludge attack blinds them boh which takes them out of the battle. Ash decided to send out his newly caught Pidgey.

Pidgey dodges both Koffing and Ekans's attacks before Ash orders "Quick Attack" Pidgey goes into a Quick Attack. Ekans avoids the attack by going underground, forcing Pidgey to come to a sudden stop. Koffing fires an ordered Smog attack by the first Poacher, which Pidgey splits with its wings. Pidgey dodges multiple Sludge attacks and Ekans's retaliation. Despite soaring high in the sky, both Ekans and Koffing manage keep up with Pidgey. Ash orders "Gust" The Gust attack missed Koffing. Suddenly a harsh double Tackle attack takes Pidgey out. Ash recalls Pidgey and Ash decides to send out Caterpie to battle. The sight of the bug simply amuses the two Poachers as they prepare to attack. Ash orders "Fire String Shot" and the attack completely incapacitates Koffing and Ekans. Caterpie rushes into a Tackle attack on Koffing which sends Koffing into Ekans and thus taking them both out, shocking everyone.

The second Poacher shouts "Let's just get them" and the two of them point their hunting rifts at the three of them. The two Poachers are knocked out by sweep kick sent by Isabella.

The Collector said more confident "I have you now, Isabella get them" Isabella smirked attacked Eve. Both were evenly matched as they fought hand to hand. The Collector tried to seize Lilly while Ash was distracted when The Techno Samurai came crashing through the trees fixated on Lilly. The Collector fled at the superior foe. Ash was knocked out of the way of a net sent by The Techno Samurai by Eve. Isabella took this as a sign to withdraw and return to her employer. Eve grabbed Ash and ran. The Techno Samurai chased Eve and Ash through the trees to a cliff face. It slowly advanced on Eve and Ash. Lilly glows purple again and a blast of purple lighting hit The Techno Samurai dead on. Eve looked delighted at the development.

She muttered "Thought there be side effects"

Ash asked "What was that?"

Eve said hiding a few things "As I told you I worked for The Techno Institute. One of the things they were working on was Project L"

Ash asked "What was Project L?"

Eve said "Project L was part of Professor Technology's master plan to create a very powerful Pokémon. I set the project back when I stole all the data for it" She indicated The Techno Samurai when she said "But with that robot fixated on capturing her then they still haven't given up. As I said there are some very powerful villains out there" She and Ash leave the area where The Techno Samurai remained. She continued "The Techno Institute will stop at nothing in advancing science and technology not caring for their effect on the natural world thus causing the rise of a eco terrorist group known as Team Nature" They return to the stump where they had set up camp. Ash released Caterpie while Eve sits on the ground.

He congratulates Caterpie on coming through by saying "Good work Caterpie" Caterpie smiles and Lilly licks Ash's ear. At that moment, Caterpie begins to sprays mist from its mouth, startling Ash half to death. The mist covers Caterpie, signaling evolution. Caterpie then evolves into Metapod. Ash's Pokédex than notes that it has reached this stage more quickly than any other Caterpie on record. Eve looked impressed.

She said "Well done"

Ash smiles and pats Metapod on the head and says "Excellent work"

"Time to head to Pewter City, I think before we get in trouble again"

"Too Late" said another Poacher as he and a gang of other Poachers surrounded them in a circle pointing hunting rifts.


	4. The Hunters of Viridian Forest Part II

**Do not own Pokémon**

 **Each chapter is based around an Episode of the anime.**

 _ **UPDATE: Story Changes + Additions / Spelling and Grammar Checked**_

 _ **Renamed from Viridian Forest Part I**_ I _**to The Hunters of Viridian Forest Part II**_

 **Lilly's Story: The Indigo League**

 **Chapter 4: The Hunters of Viridian Forest Part II**

Zana awoke to find herself in a cage with an already awake Gerald who she did not know the name off. They looked out of the cage to see a tall girl wearing green body armor with a green helmet covering her head talking into a video phone. Zana couldn't see who was on the other end of the call or could hear what they were saying. Gerald was a nervous mess disgusting Zana. Zana saw a flash of green in the distance and so did the tall girl who went to investigate.

Ash and Eve found themselves surrounded in the center of a circle of Poachers pointing their hunting rifts at them. The Head Poacher said "You had to meddle with us didn't you"

He demanded "Give me all of your Pokémon and we let you live"

Ash replied with "Never" Eve looked unconcerned.

The Head Poacher said smiling "I challenge you to a Pokémon Battle and if I win you will go back to hand all your Pokémon to me"

Ash said "And if I win"

The Head Poacher said "I will never lose" and he meant it as if he did lose then his lackeys will act.

Ash said with no choice "I will fight you"

The Head Poacher said pleased "Excellent" He released a Pinsir.

Ash sends out, Pidgey. The two then battle for some time as they were evenly matched and caused to Pidgey evolve into Pidgeotto. The Head Poacher was getting frustrated but to his delight Pinsir finally manages to defeat Pidgeotto by accident. Ash then thought about who to send out next. He decided to send out Metapod. Ash then orders "Harden" Metapod breaks Pinsir's pincers with Harden to win the round. The Poacher then sends out his own Metapod. Ash then orders "Harden" again and The Poacheralso orders "Harden" The two Metapod continue to use Harden for a while causing everyone to become bored. Their boring battle was interrupted by The Techno Samurai crashing through the tree causing everyone to freeze. This time being under the control of The Collector who was flying in another flying machine with Isabella behind it.

The Collector said "boo" causing The Poachers to run in fear, he then turned to where Ash and Eve were to find them missing. He growled in frustration and Isabella just snickered.

Eve dragged Ash away during the distraction and nothing much happened during the rest of the day until they set up camp and Eve wanted to chat with Ash. Ash said to Eve "Yes"

Eve said "Good work today with dealing with your first real villain" Ash noticed that her emotionless eyes were showing a trace of pride.

Ash said "Thanks"

That night Lilly was awoken by beautify singing that echoed throughout the forest. She was enthralled by the singing so she followed it into the center of forest where everything was glowing green. A female with green hair and kind green eyes was sitting on tree stump singing. The female saw her and said lovingly and motherly "Hello Little One, I'm Nature" she beckoned Lilly to come over. When she did, Nature picked her up and said "Hard to believe one as little as you have the power to defeat The Techno Institute's Abomination" She said seeing Lilly confused face "Speak Little One"

Lilly said in a childish female voice "What do you mean" and Nature understood her.

"Well Little One, your egg was taken by the soulless Doctor Order as part of her ex-master's masterplan. She did something to link with the specimen we called The Abomination. How I don't know. I do however know that fragile balance of nature and technology is being destroyed by the ex-master who is obsessed with technology and doesn't care if he destroys the natural world" Nature then said sadly "The time will come you will face The Abomination in battle to restore the balance but time is not on your side as my rage over the destruction can only be contained for so long. When my followers summon me fully, I will not be able to contain my rage any longer and will be blinded by hate" Her voice weakened to whisper and the glowing green faded. Lilly founded herself sitting on the ancient coffin that the crew of people in black with a green N on their chest recovered from the unmarked grave. Nature's voice said "I will see you soon, Little One" as the green glow completely disappeared. Lilly felt the air become colder and she hid in a nearby bush. The man with short white hair and blue eyes wearing a black suit and black glasses with black tinted lenses walked into Lilly's view.

He knelt in front of the coffin and said "Milady, my men have found a power source for you to use"

Nature voice echoed "Excellent work, Winter" Her voice was now cold and harsh instead of lovingly and motherly. She asked impatiently "Well what is it?"

"Well, it is called The Moon Stone. All we need to find where it is located within Mount Moon" said Winter as Lilly crept away. However, Lilly was grabbed The Collector.

Early the next morning, Ash awoke to see Lilly missing. He was intermediately worried. In his frantic search, he suddenly had a feeling where Lilly was. He followed the feeling and found Lilly in a small near a larger destroyed cage. Ash saw Lilly was crying and it made him angry. He snuck up to the cage passing The Collector who was messing with The Techno Samurai.

Ash is nearing where Lilly was when he was knocked to the ground by Isabella. Isabella said "Sorry kid, nothing personal"

The Collector said "This is the last time you mess with me" as The Techno Samurai absorbed him. The Techno Samurai then morphed into a Mecha-Machop, a giant robot version of Machop that was about the same size of the Mecha-Meowth but with The Collector inside controlling it. The Collector said via the robot voice of the Mecha-Machop. "Try to stop me now"

Meanwhile on a cliff overhead, Winter was watching while a few of his men, the people in black with a green N on the chest were carrying the ancient coffin out of the forest so they can take it to Mount Moon and couple of other men dragging along an unconscious Zana. He said to himself "This is an interesting turn of events" He clicked his figures and the swarm of angry Beedrill that were glowing slightly green came flying out of the trees. He ordered "Take out that robot monster" taking the opportunity destroy the horrid technological terror. He then followed his men.

Ash was forced to retreat as the Mecha-Machop was trying to crush him with its fists. Metapod came out of his ball to save Ash by firing a String Shot making the Mecha-Machop foot get stuck on the ground.

The Collector said via the Mecha-Machop "Ah your weak Pokémon can't stop men" The Mecha-Machop left fist knocked Metapod aside into a tree. "Look how it easy it was to defeat it" Ash watched Metapod begins to glow and evolve into Butterfree. Butterfree used Stun Spore causing The Mecha-Machop to lock up. At this moment the swarm of angry Beedrill that were glowing slightly green attacked The Mecha-Machop. Eve arrived to see this. Isabella just watched as this was happening.

Eve asked Ash "Are you alright?"

He said truthful "I'm fine now" He freed Lilly who was looking at him worried. Ash said to Lilly "I'm glad you ok" He look at Butterfree and smiled happy. Ash recalled Butterfree. They walk away just as The Mecha-Machop exploded causing The Collector to go flying. The swarm of angry Beedrill disappeared to where they came from.

Ash, Lilly and Eve then make their way out of the forest and onwards to Pewter City not realizing that they took the path that avoided a one-sided fight between The Poachers and Team Nature in The Poacher's base camp. The Poachers were no match for the Team Nature Grunts.

Near Pallet Town, the hooded female figure was crouching outside of Oak's Lab waiting for Professor Oak to leave so she could use his computer to hack The Techno Network. She was overhearing a radio saying "Chairman von Nuclear has announced that The Techno Steamship will stop at Vermilion City. In other news, a man in hooded black robes wearing a skull mask has been seen at Pokémon Tower around The Unknown Tomb. The Techno Institute has issued a warning that the man is linked to a cult in Kalos Region so please do not approach if you see him" The radio was silenced as Professor Oak turned it off. Professor Oak left the lab and locked the front door a few minutes later. The hooded female waited for a few moments. She then picked the lock and entered the lab. She headed over to Oak's computer and hacked into it. Then she skilfully hacked into the network silently thanking Doctor Order who had told the easiest ways to hack into The Techno Network. Looking through the files stored she came across the sighting of her pichu in Viridian city and then the Forest. Using another trick taught by Doctor Order, she erased all data contained about Project L and Project M2. She exited Oak's Lab with the file and headed off into the trees towards Viridian Forest wanting her pichu before The Collector or The Techno Institute get their hands on her.


	5. The Faceoff Against Gary

**Do not own Pokémon**

 **Each chapter is based around an Episode of the anime.**

 **UPDATE: Story Changes + Additions / Spelling and Grammar Checked**

 **Renamed from Pewter City Faceoff to The Faceoff Against Gary**

 **Lilly's Story: The Indigo League**

 **Chapter 5: The Faceoff Against Gary**

On Zeus, Captain Zed was talking to Professor Technology on a video screen. He was saying "Professor Technology, Captain Zed reporting in"

Professor Technology just said "Report"

"Our network was hacked and all research has been erased" reported Captain Zed "and we also lost The Techno Samurai prototype and the link to Agent Green"

Professor Technology said "No matter we don't need the data anymore and The Techno Samurai has served its purpose. Agent Green can be bought in and relinked as soon as we find it"

Captain Zed decided to mention "What do can I do about Team Nature"

Professor Technology said "Don't worry about them yet. I have made sure Zeus has been isolated and if Zeus isn't compromised then we still have the edge" He ended the communication. Captain Zed got back to tracking the stolen tech used by The Collector in tracking Project L.

Elsewhere, Two Techno Policemen were digging a hole on orders of their leader Captain AJ. They were thinking about how suddenly in the last week that The Master Plan was moving forward faster than originally planned. They were proud that The Techno Institute was so powerful that their enemies; Team Nature in Kanto, The Church of Arceus in Sinnoh, The Liberation Party in Unova and The Blood Cult in Kalos could not stop them. Operation Pewter City was the first of many stages in the complete takeover of Kanto by The Board of Executives. They then heard something and they hid. A seventeen-year-old boy with brown hair and brown eyes fell in.

Ash, Lilly and Eve have reached the edge of Viridian Forest and arrive on the outskirts of Pewter City. Ash was glad that they weren't held up by something else and tired enough that he decided to take a rest on some conveniently placed rocks on the outskies of Pewter City.

Ash asked Eve as he rested "is there more you can tell me about The Techno Institute?"

Eve said somewhat rambling "The Techno Institute was responsible for a strange woman believing that she was the incarnation of mother nature after being experimented on by Professor Technology and Doctor Order. She was freed by an employee by the name of Winter Frost alongside the woman's triplet daughters. This caused Chairman von Nuclear to take some control of The Techno Institute from Professor Technology" She then asked "Do you know the so called Super Storm the hit ten years ago?"

Before Ash could reply with a yes, a man appears with tray of rocks and tells them "There is a fee for sitting on these rocks" Ash got up and groaned. The man then says introducing himself "I'm Flint" He then asked "Does anyone want to buy rocks or gems as souvenirs from Pewter City?" Flint was man wearing a red hat covering his eyes and a fake beard. Neither Ash or Eve was interested in buying a rock. However, Lilly had somehow managed to get a little black diamond out of Flint's box of stones and gems that he had placed on the floor when he had arrived. Flint said "You touch you buy" so Eve handed over some money and then tied the black diamond up in some string. She put it around Lilly's neck.

Eve said "There you go, prettier already" as left a happy Flint and headed to the Pokémon Center. Both Lilly and Ash are surprised to encounter Nurse Joy again.

Ash says "Hello Nurse Joy what are you doing here, I thought you were in Viridian City"

Nurse Joy looks at him and explains "I'm not the Viridian City Joy you met, but her older sister" Ash and Lilly nodded. Ash then felt slight foolish as he thought that Eve knew it. Nurse Joy then showed Ash a poster promoting a tournament called the Pokémon League Championship and says "This is probably the reason you are here" Ash immediately decided to sign up.

Ash inquired "How do I enter?"

Nurse Joy said "Before you can enter, however, you will need to defeat the eight Gym Leaders endorsed by The Techno Institute and earn all of the Gym Badges as proof of victory" Flint walks in at this point and tells Ash skeptically "The Pewter City's Gym Leader, Brock is strong. You don't have a chance of winning against him" He laughs scornfully at the very thought of it. Ash stormed off while Lilly snugged him to cheer him. Eve it blocked from leaving by Flint.

Nearby The Collector and Isabella in a flying a machine flew over The Pewter Museum of Science. The Collector said handing Isabella a small ray gun. He said "Be careful when using The Genesis Gun to not break it as I haven't go anymore Techno Technology to use and this is the most versatile of what I stole"

Isabella said "Whatever" as she jumped off the machine. She entered the building. She pointed The Genesis Gun at the Fossils of Aerodactyl and Kabutops displayed. She shot a blast of red causing Fossil Aerodactyl and Fossil Kabutops to come alive. They started destroying everything until they became under the control of The Collector.

A few moment later, Ash standing outside the gym when Eve finally reappeared, Ash asked her "Where were you?"

Eve said "Just having a friendly chat with Flint, here is your healed team" she handed him his team. Upon entering they find it empty.

Ash calls "Anyone there"

The voice of Gary said "Late again Ketchum, he just left" Ash frowned as something was off about Gary's voice but he couldn't place it. Gary emerged from the shadows. "I challenge you to a Pokémon battle, Ketchum"

Ash says determined to beat Gary "I accept"

Gary said as Lilly got into a fighting stance "A Pichu, very cute but it will be no match for me" Lilly smiled at being called cute but was angry at being called weak. Despite what Gary said, Ash begins the match with Lilly while Gary starts off with an Onix. Lilly glared at Onix, Onix looked slightly intimidated.

Ash said "Attack" Lilly used Disarming Voice. The attack is dodged.

Gary commands Onix "Counter with Bind" Onix tries to crush Lilly but Lilly was too small and escaped. However, they are interrupted by Fossil Aerodactyl crashing into the gym.

The Collector voice boomed "I got you now and this time I mean it" Fossil Aerodactyl grabbed Lilly

Ash ignoring Gary ran out with Eve. As Ash and Lilly were leaving the Gym, they encounter Flint. He stopped Ash from following Eve.

He said after asked him glancing at the retreating figure of Eve "How well do you know your friend Eve?" Ash tried to leave but Flint grabbed his arm.

Ash said "Not very well" hoping Flint would let him leave.

Flint said looking unhinged "She is…." Flint looked around making no sure Eve didn't appear from nowhere "…Doctor Order. She is a completely evil being created by Professor Technology"

Ash did not believe him so he said "Eve is not evil"

Flint said looking even more unhinged "She is Doctor Order I swear it. I recognized her anywhere"

Ash interrupted with "Why would you"

Flint said "I used to work for The Techno Institute and I was there when they created her, I will know her anywhere" Ash managed to break free and he ran off towards where Eve went. Flint shouted "I am warning you as while Doctor Order has no emotions or doesn't really understand them, she is very good at manipulating people to do her bidding" Ash found himself themuseum to see Eve trying to fend off Fossil Aerodactyl. The Collector was holding Lilly with a grin. Fossil Aerodactyl grabbed Eve and flew off with her. Ash quickly released Butterfree and Pidgeotto.

He said to them "Save Eve" He watched as they tried attacking Fossil Aerodactyl but it just shrugged off the attacks. He watched Butterfree and Pidgeotto then worked together to keep attacking one spot. Fossil Aerodactyl fractured apart as it was still only made of fossilized bones.

Eve fell and Ash managed to catch her before she crashed into the ground. It did knock him to the floor but did not cause any serious injury. Eve did look shocked.

The Collector said "Bah, I still have the other one as Fossil Kabutops came crashing out of the ruins. He said "Attack them" Fossil Kabutops advanced and Lilly bit The Collector's hand causing him press a button accidently and he crashed into Fossil Kabutops destroying it. Lilly ran back over to Ash who scooped her up. Butterfree and Pidgeotto were recalled. Ash took Eve who was still in shock back to The Pokémon Centre. Ash helps Eve to a room and they spent the rest of day within the Pokémon Centre while Eve was recovering from shock.

The next day, when Ash goes down to the main part of Pokémon Centre, he sees Eve watching a TV. A Reporter was standing in front of the ruined museum building saying "The Techno Institute has blamed the attack on The Pewter Museum of Science on the wanted criminal Isabella Black who witness claim to have seen resurrect the fossils". The Reporter continued with "recapping our other stories, People travelling through Mount Moon report shady figures in the area so caution is advised and the man in hooded black robes wearing a skull mask once again has been sighted around Pokémon Tower"

Ash asked "Are you alright?" sitting next to Eve.

Eve said not looking him the eye "Thank you for saving me for yesterday" before ranting "Look at that someone has covered up the involvement of The Collector. It must be the influence of his wealthy father"

Ash decided to ask "How do you know so much?"

Eve looked around and seeing no one said nervously "When I told you I worked for The Techno Institute. That was only half the story, I was created by Professor Technology in attempt to mimic organic life"

Ash asked confused "Meaning?"

"I am a very advanced AI within an advanced robot body that Professor Technology has tried to replicate many times" said Eve looking away from Ash. "I stole the information from the computer when I managed to break free"

Eve looked dejected so Ash said "You are still my friend, no matter if you are a machine and that would explain your eyes"

Eve said shocked "You don't think that I am soulless evil machine"

Ash said "Not really"

Eve said smiling "You are then one of a kind" Ash, Eve and Lilly then leave the Pokémon Centre with Eve looking more upbeat. Gary was however waiting for them.

He said "We got a battle to finish". They went back into the gym and He released Onix. Ash sends out Butterfree.

Ash orders "Sleep Powder" and Onix falls asleep to Gary's frustration. Ash switched out Butterfree and Lilly jumped out. Lilly used Disarming Voice but Onix was hardly hurt. Ash said "Use another attack" Lilly used Hidden Power and Onix tried to dodge but he was hit. Onix fainted and fell right onto Gary. Ash ran over to him and saw wires sticking out of him.

Eve said commenting "That not your rival, that is one of Professor Technology's creations. He has certainly improved" The faux Gary rose and tried to grab Lilly. Eve was faster and punched him in the chest knocking him out and a Boulder Badge fell out the robot's pocket. She said to herself "What does he want the badge for?" She then handed it to Ash. Ash did not want to accept it but Eve said "You deserve it. You won against him in battle and the real gym leader is gone. Plus, it is a reward for yesterday when you displayed heroism" Ash took the badge knowing Eve would force him.

Flint come crashing into the gym with anger in his eyes. He grabbed Eve not caring if he hurt her. He screamed "I found my son, you tried to kill him"

Eve said with fear in her voice "I don't know what you are talking about"

Ash said standing up for his friend "She hasn't done anything, it more likely the fake Gary here" He pointed to where the faux Gary had been but now had vanished.

Flint said not looking where he pointing "Nice try kid, I know it was her" Eve kicked him right in his most sensitive. He dropped her and Eve dragged Ash out of the gym before Flint recovered. They quickly leave the city and head toward Mount Moon leaving an angry Flint.

The hooded female was searching Viridian Forest when she stumbled into the abandoned ruins of camp that had belonged The Poachers. She did not bother glancing at the site. She did pause when she spotted the tall girl that wore the green body armor with the green helmet that covered her head laying on the ground on edge of the camp. The hooded female recognized it one of Professor Technology's new robot minions. She started reprogramming the robot to work for her as fighting Professor Technology would require help.


	6. Mount Moon

**Do not own Pokémon**

 **Each chapter is based around an Episode of the anime.**

 _ **UPDATE: Story Changes + Additions / Spelling and Grammar Checked**_

 _ **Renamed from Winter and The Moon Stone to Mount Moon**_

 **Lilly's Story: The Indigo League**

 **Chapter 6 Mount Moon**

Inside the Mecha-Vespiquen, a giant robot Vespiquen that was the size of a large mountain, was Captain AJ, a green haired man in the Techno Policeman outfit. The Mecha-Vespiquen was hovering over the sea when Captain AJ was contacted by Professor Technology on a video screen. Professor Technology said "We have removed Brock so you are a go for Cerulean City. At this rate, we should complete our master plan in no time"

"Excellent News" said Captain AJ

Professor Technology then added "I want you to stop at Mount Moon to recover The Moon Stone as with that kind of power, we will no longer rely on Nuclear Industries for our energy needs"

Ash, Lilly and Eve were hiking toward Mount Moon with Ash glancing back to see if Flint was following them. Eve was saying rather factual "You know there was a legend that a meteor called The Moon Stone crashed into this mountain in prehistoric times. It is said to contain unknown powers that some evil teams would kill for and rumored to still be deep within the mountain" As they were walking the air grew colder.

Ash said "Maybe we will see it" as they reach the foot of the mountain. As they reached the foot of the mountain, it started snowing. Ash noticed that Eve was frowning.

He heard her say "This is unnatural snow" but before he could ask her expand her comment, A brown-haired man wearing a lab coat wearing glasses was chased out of a cave by a flock of Zubat were glowing green. Ash released Butterfree and put the flock of Zubat to sleep.

The man says "Thanks for that, I am Seymour, a researcher from the Pewter Museum of Science and I am studying this mountain. Anyway, the weather around here has grown colder over the past day and now it started snowing. This is disrupting the Pokémon who live inside. On top of that some of them seem to be under some short of mind control. This prevent me getting into the mountain to do my research on the Moon Stone"

Ash asked "What is the Moon Stone?" Eve rolled her eyes.

Seymour said "It is a massive stone which is believed to be thousands of years old or even more. It is said to be hidden in the mountain. Fragments of the main stone evolve certain Pokémon like Clefairy. I theorize that this is because this stone contains the powers of Arceus" as he leads them into the caves of the mountain.

As they walk Lilly starts to feel a pull in her heart. After a few hundred meters, Lilly starts to feel the pull even stronger and her will and strength were weakening. A Clefairy then bounces past, carrying something. Seymour told them "That is a Moon Stone fragment" Ash scans it on his Pokédex and decides to catch it, but Seymour stopped him by saying "it's better to let them be" The Clefairy then gets trapped in a net be held by a Team Nature Grunt, a man in black with a green N on the chest. This Grunt was followed by a two other Grunts that appeared out of the shadows.

The Head Grunt says "Look who we have here, some twerps" He laughs and starts to leave with the Clefairy.

Ash then said "I challenge you to a battle"

Eve said grabbing Ash's Arm "Don't, they are from Team Nature. They have supernatural powers granted them by their leader who was the woman who believed she the incarnation of mother nature that I told you about"

Ash after hearing this Ash feels more determined to beat them and Seymour agrees by saying "We have to stop Team Nature before they make any more trouble or cause permanent damage to the mountain ecosystem"

The second Nature Grunt freely admits "Our boss is response for the snow and for controlling the Pokémon in the area"

The last Nature Grunt even says "We want The Moon Stone so to resurrect Our Mistress and no one not even The Abomination created by Professor Technology can stop us from reaching out goal of a technology free world"

The Nature Grunts eyes glowed green freaking everyone out and they summon three Paras. The Pokémon were glowing green which made Ash realize that The Zubat and The Swarm of Angry Beedrill had been controlled by Team Nature. Ash calls Butterfree.

The Head Nature Grunt orders The Paras "Attack them" The Paras attacks with Stun Spore but Butterfree counters with Whirlwind. This turns the Stun Spore back on The Team Nature Grunts, much to their surprise. This causes The Head Grunt to drop the net and the Clefairy to flee and Lily who jumped off Ash's shoulder to follow the pull then fled as well. Seymour disappears as The Head Nature Grunt gets paralyzed which caused Eve to chuckle.

The Paras then try and attack Butterfree but Ash asks Butterfree "Another Whirlwind to blow them all the way out of the cave" The two remaining Nature Grunts blast off into a wall.

On the peak of Mount Moon, Winter was sitting cross legged on the group while a group of Nature Grunts wearing fragments of the moon stone were dancing around the ancient coffin with Zana tied to it. She was covered by a green glow and surrounded by circle of ancient runes. Winter was exercising his power to search for power signature of the main moon stone. He suddenly ordered his men within the mountain towards where the stone was located.

Elsewhere Lilly was travelling though small tunnels, only big enough for her, towards the source of the pull in her heart. She exited the tunnel to find herself surrounded by a large group of excited Clefairy. They lead her to the Moon Stone, one of Clefairy said to her "Go and speak with The Spirit of The Moon.

The moon stone glows and a ghostly figure of a large Pokémon resembling a skeletal, legless bat appeared in place of the stone. It has a short snout, dark pink eyes, and a deep blue area on its upper head that shows a constantly changing starscape. A rigid, raised hood wraps around its head in a crescent shape and drapes around its neck as well. The outside of the hood is yellow, while the inner part that curves around its head is a pattern of deep blue and white streaks. Its torso resembles a ribcage with a slightly curved spike on each shoulder and three spikes extending. The bottom of its tail is lined by a yellow crescent, with a ridge running up the middle of the tail towards the ribcage. "I am Lunala, emissary of the moon" greeted Lunala, The Spirit of The Moon in a female voice. "I am happy to meet you at last"

Lilly said confused in her childish female voice "You are?"

Lunala said "Yes. We have been watching on The Creator's behalf, I watch during the night and Solgaleo during the day. I am only able to talk with you as this fragment came from the moon when it crashed into this planet becoming said moon. We have seen events moving towards this day. The follower of Chaos, The Chairman manipulating The Professor in creating The Soulless One, The False God, The Abomination and The Duplicate to generate chaos. The Professor gave you power that you shouldn't have in the first place to control The Abomination after The Soulless One escaped his control in her desire to bring Order to the Chaos". Lilly grew afraid that The Spirit of The Moon would take that power away. Lunala said to reassure her "The Creator will not take it away. Events of the future will require them. Stopping The Abomination is only one of the tasks you have to face. The Chairman and his unwitting minions, The Professor, The Soulless One and The False God must be stopped to prevent Chaos taking over"

Lilly said "Why me?"

"Chaos has weakened The Creator and only you and The Chosen One can defeat The Chairman and in turn Chaos's plans. Come closer" said Lunala. Lilly complied and after a flash, the black diamond amount her neck was glowing the same colour of the moon stone which had reappeared in place of Lunala. Lilly found herself once again surrounded by excited Clefairy.

Elsewhere an angry Flint was in a room under his house messing with an old communicator. He knew that Doctor Order was behind his son Brock's injury. He dialed in the old number hoping that his old ally would answer as he was the only man who could help him to stop Doctor Order. He was relieved when Chairman von Nuclear voice said "Flint, good to heard from again, what do have to report this time"

Flint said "I have seen Doctor Order"

Chairman von Nuclear asked "Where?"

Flint said "Doctor Order is travelling the kid and the Spiky Eared Pichu you told me to keep an eye out for. I fear she is trying to take over again"

"A Spiky Eared Pichu you say" said Chairman von Nuclear pleased "In that case I would like to speak to you personally. Meet me at Viridian Gym"

Later, Eve was feeding all the Pokémon including the Clefairy that they saved from Team Nature with Pokémon food made from her special secret recipe. Ash was fretting that Lilly was gone but Seymour reassured him when he said "The Clefairy will look after her" Lilly walks into the little campsite and caused Ash to relax. Lily jumped back onto his shoulder. Ash goes over to where Eve was standing staring unblinking at The Clefairy. He says concerned "Eve" a few times to get her attention.

Eve eventually replied with "Yes"

Ash asked her as he is concerned "Why do you stare off into space"

Eve said hiding something "It's a glitch in my system and I afraid that I can't do anything about it as it was caused from breaking away from Techno Network"

"What did you mean by unnatural snow?" asked Ash changing the subject realizing that she wouldn't tell him everything"

Eve said "The snow is not created by natural means. It is created by Winter Frost who gained this powers from messing with his own genetics"

Ash said "So He is here somewhere"

Eve said "Yeah, He leads these fools now" At that moment Clefairy decides it time to leave. Eve said "Lets follow them" and so the group follows the Clefairy. A few hours later they arrive where The Moon Stone was to see instead of Clefairy, a group of Nature Grunts wearing wooden Clefairy face masks dancing around the stone as a beam of light was diverted to the ancient coffin with the girl tied to it. Eve said fear as she saw the coffin "No, it can be" She dropped to floor terrified. A smirking Winter appeared from the shadows. Seymour and Ash are grabbed from behind by Nature Grunts while trembling Eve is picked up by a joyful Winter.

Winter said with a sneer "Look who we have here" He said an evil grin "You thought she was dead didn't you when you hid the coffin. You will be the first to face her wrath when she returns to this plane of reality. You will suffer greatly I will assure you"

Ash said "Stop it" trying to defend Eve who was frozen in place.

Winter said chuckling "Look here. Some puny kid is trying to help" He turned his head to look at Ash. "Listen Kid, you wouldn't help her if you knew what she is responsible for"

Suddenly he dropped Eve to the ground and said to his men quickly "We got what we need here" His eyes glow green and A Froslass appeared. "See you soon Eve" He said as Froslass disappeared with him. The Nature Grunts and the coffin vanished after everyone was blinded by a flash of green. A faint buzzing that steadily grew louder was heard.

Seymour said "Follow me" as red eyes appeared in another tunnel. Everyone ran and Ash looked behind him to see robot version of a Pokémon he recognized as Combee. The Mecha-Combee swarmed around The Moon Stone.

Ash and Eve followed Seymour through the mountain. He led them outside and they saw looming over the mountain, the gigantic Mecha-Vespiquen with Mecha-Combee carrying The Moon Stone pouring into it. Distracted by this, they did not see a pair of Giant Mecha-Combee grab Eve. Ash released Butterfree and Pidgeotto but they were blocked by a group Mecha-Combee. Ash watched ash as Giant Mecha-Combee brought Eve into Mecha-Vespiquen. The Mecha-Vespiquen then flew off. Ash did not notice that Seymour had disappeared. Ash started walking in the direction where The Mecha-Vespiquen had gone which unknowing for him was Cerulean City.

Gerald was lost inside Viridian Forest after the strange man let him go. Gerald walked into a clearing to find a tall boy in red body armor with a red helmet that covered his head. Gerald paled and backed away but the boy said in robotic voice "Halt" Gerald stopped moving. The tall boy advanced menacingly.


	7. Takeover of Cerulean City

**Do not own Pokémon**

 **Each chapter is based around an Episode of the anime.**

 _ **UPDATE: Story Changes + Additions / Spelling and Grammar Checked**_

 _ **Renamed from Attack on Cerulean City Part I to Takeover of Cerulean City**_

 **Lilly's Story: The Indigo League**

 **Chapter 7 Takeover of Cerulean City**

The Mecha-Vespiquen flew over Cerulean City causing a shadow to fall over the city as it blocked the sun. Everyone to stared up into the sky at the giant robot in mix of awe and fear. Inside the head was the control room. This was where Captain AJ and his pilots controlled the Mecha-Vespiquen. Captain AJ said to his men "Activate the speakers"

A Techno Pilot, a man in a while pilot's outfit said "Yes Captain" and pressed some buttons.

Captain AJ said in the microphone "People of Cerulean City, The Techno Institute in now in control of the city until further notice. We like to thank you for your cooperation" He then said to Techno Pilots "I am going to interrogate our new prisoner, only disturb me if something bad happens and call Seymour and give him my report" He left the control room.

A few hours later, Ash, managed reach Cerulean City where he saw The Mecha-Vespiquen still looming over the city. Ash walked through the eerily empty street when he suddenly jumped when a small ring comes from his bag. He picked up the Pokégear-Zero and said "Hello"

Eve tired sounding voice asked "Ash where are you?"

Ash said "In Cerulean City"

Eve said "Excellent. Travel to my old workshop near the gym and enter the passcode 5 15 14 into the control panel"

Ash asked "Will you be alright?"

Eve said "Oh I be fine and don't worry about The Collector bothering you, I think he was captured as well. I contact you again when you get to my workshop" She added in a quiet voice "Be careful and try and get out of there as soon as possible as I think The Mecha-Combee randomly patrol the city"

In another part of town Isabella was sneaking through town, annoyed that her contract stated that she had to save The Collector from The Techno Institute. She snuck into an old house with a symbol of eight arrows in a radial pattern on the door. She typed in the password in the keypad in the room under the stairs. A video screen appeared with a shadowy man sitting on a large chair. He said "Bella good to hear from you again. Is your employer giving you any trouble?" He added on concerned.

Isabella said "I need your help C. The Techno Institute has captured my employer and due to the dam contract, that you sold him, I am required to save him"

C said "Don't worry Bella, I will help you for a price of course"

Isabella said "What is C?"

C said "I want your contact when it has run out with Victor, I need people like on my payroll. my buddy, Victor's father regards your skills highly and he is a hard man to please"

Isabella said even knowing the factor that C was more dangerous employer then The Collector "Of course"

Ash meanwhile was walking when he saw a group of Mecha-Combee heading towards him. A female robotic voice said through them "This city is now under my control and order will be maintained" Mecha-Combee paused when they saw him. Ash and the group of Mecha-Combee stood facing each other. It was broken by Mecha-Combee falling to the ground deactivated. Ash saw an orange haired girl holding a strange device. She grabbed Ash and ran for it as more Mecha-Combee poured out of the Mecha-Vespiquen. The girl took them down an alley way that was blocked at one end. Another girl said, "In here" and a door that Ash didn't notice opened the orange haired girl pulled here inside. Inside what appeared to be a warehouse was a group people wearing a weird uniform

The orange haired girl said "I am Misty and this is Cerulean City Resistance"

"What Happened Here?" Ash asked

Misty said "Well The Mecha-Vespiquen under the control The Techno Institute arrived and said it was in control of the city. We weren't too worried until ten minutes later when Mecha-Combee poured out of the Mecha-Vespiquen and female voice that called herself Doctor Order said she is control now. Dozens of people were abducted and returned under some form of mind control. I formed Cerulean City Resistance to stop Doctor Order before The Techno Institute launches a laser strike from Zeus"

Ash frowned and asked "Zeus?"

Misty said "A space station owned and ran by The Techno Institute"

Ash said getting back on track "I need to get to a workshop by the gym where my friend who is aboard the Mecha-Vespiquen can help us stop it"

Misty said "Are you sure that you can help stop Doctor Order?"

Ash said "Yeah"

Misty said "Then I will help as it is the only plan we have at the moment" She handed Ash an ear piece. "I would go with you but we will be distracting the Mecha-Combee so you don't get caught" Ash put it on. Misty opened a door at the other end. As Ash was leaving he hear Misty say "Good Luck" He headed out and followed the directions that Misty whispered in his ear and he made it to Eve's Workshop. He went to the door and entered the code. He entered the building. The ear piece went silent but Ash did not notice. What he found surprised him. He found Isabella standing in front of an exact double of Eve apart from having red hair who was growling. They both spot Ash and Lilly. Lilly looked at the girl in the eye and the girl then looked at Ash.

"I'm a friend of Eve" said Ash

The girl said "I believe you" before turning to Isabella.

Isabella said "You need my help to defeat Doctor Order and you both know it. My friend C said Doctor Order has taken control of all of Techno employees on board on top of an endless supply of Mecha-Combee"

Ash asked "Why should we trust you?"

Isabella said "Because I as Isabella Black keep my word and beside my actions towards you are just business. In fact if it makes you feel better, I promise to not steal Lilly until we meet again after this incident" She put her hand out. Ash walked over to her with the girl watching to make sure Isabella did not do anything. Ash shook her hand.

He said "Deal"

Eve's voice came through the computer "Ash Are you there?"

Ash said "Yeah I am alongside Isabella Black and…"

"So you met Eon, She is very protective of me" He heard Eve say with hint of fondness.

Eve said with pride "I will teleport you inside then we can shut it down"

Ash enquired "Are you ok? I heard Doctor Order has taken control"

Eve said "I am find, I am hiding in power generator, Send Eon to me when you arrive and I will join up with you"

Inside Zeus, Captain Zed was overseeing the powering up of The Lighting Bolt, a super powerful laser on the orders of Chairman von Nuclear. It was aimed at The Mecha-Vespiquen but would destroy the whole of Cerulean City. Chairman von Nuclear wanted to destroy Doctor Order for once and for all so went over the head of Professor Technology using his full powers as chairman to make sure. Captain Zed did as he asked despite firing The Lighting Bolt will use nearly all of Zeus' power for one shot. It would another day or so for the solar panels to absorb more power. He watched as the laser slowly powered up.

Ash blinked and suddenly found that he, Isabella and Eon were standing inside a metal corridor. Eon said "I will get Eve while you find a way to regain control of this station". Eon disappeared up the corridor so Ash and Isabella went the other way. After a few minutes of walking he peered around a corner to see two blank looking Techno Policemen guarding a door.

Isabella said to Ash "I will deal with them" She quickly took them both out in a sweep kick. and Ash entered the room to see Captain AJ with gold glowing eyes at the other end of what appeared to be a battle arena with a swimming pool in the center. He was behind a forcefield. The door locked behind Ash locking Isabella out.

Doctor Order said through Captain AJ said "We meet at last, Ash Ketchum. I been watching you closely since you acquired Project L. I thought it was time to introduce myself to you. As you might know I am Doctor Order, the AI that has been controlling the events to get you here. I made sure The Collector got his hands on the technology and got on the trail of The Duplicate. I leaked the location of Nature's grave to Winter Frost and used The Techno Samurai for my own ends. I engineered my takeover of this mecha and soon I will have even more power at my fingertips when The Lighting Bolt hits. But until then face the youngest of The Sensational Sisters" Misty with a blank look on her face appeared from the shadows.

Misty says without emotion "I challenge you" as she released Staryu. Ash sent out Butterfree to battle Misty's Staryu. After a few minutes, Butterfree gets knocked into the water, causing it to lose the battle. Ash sends out Lilly. Staryu tried to attack but Lilly kept dodging. Lilly used Hidden Power. Staryu fainted. The Mecha-Vespiquen started shaking as a black laser from Zeus hit it. The laser was redirected to Captain AJ which destroyed him. Doctor Order laughed evilly.

Doctor Order voice said "I am now merged with The Mecha-Vespiquen and I am now unstoppable. Your purpose has been served" and the swimming pool water started to rise. "Time to Die"

As this was happening, the hooded female figure and the tall girl who had removed helmet were walking through Pewter City towards Cerulean City as the hooded female had gotten a tip of where her pichu was. The tall girl had short brown hair with brown eyes. They walked passed the ruins of the museum into an alleyway. At the other end, Damian alongside the fake Gary and a couple of Techno Policemen emerged from the shadows. The hooded female figure turned to head the other way but found it blocked by Seymour and more Techno Policemen. The hooded female said "Leaf stand down" to the reprogramed Agent Green that she named Leaf.

Damian said "You thought you escaped didn't you. We recognized Doctor Order's handy work and traced back to try and capture her. But we find out it was you who shut our satellites down and not her. A nice surprise, you been on our list for a while to require. Agent Blue arrest her" The fake Gary moved to arrest her. "Oh, and Agent Green, shut down code 233221A" Leaf became ridge and fell to the ground. He said "Don't worry we will acquire Project L soon enough".


	8. Battle for Mecha-Vespiquen

**Do not own Pokémon**

 _ **UPDATE: Story Changes + Additions / Spelling and Grammar Checked**_

 _ **Renamed from Attack on Cerulean City Part II to**_ _**Battle for Mecha-Vespiquen**_

 **Lilly's Story: The Indigo League**

 **Chapter 8 Battle for Mecha-Vespiquen**

The Collector was locked in a cell after getting ambushed by Mecha-Combee at Mount Moon while he following the kid with his pichu. He however wasn't weaponless as he still had The Genesis Gun in his possession. He would wait until he was sure to be interrogated and then he would use of one of gun's features on whoever entered. He however froze when a man clearly possessed by his secret boss and partner in his scheme, Doctor Order entered. She said coldly "Hello Victor" The Collector was scared as Doctor Order only called him Victor when she was annoyed with him. "You disappointed me Victor, couldn't even take out a single kid" The Collector trembled. "Failures like that can get you killed" Doctor Order looked at for a moment before saying "Fortunately for you, your failures are still useful to my greater plans" Doctor Order pulled in to his feet. "I need you later so don't go anywhere. I been going now as I have expected guests and don't want to be late" Doctor Order left and The Collector was relieved when she said, "Remember Collector that I will need you later" meaning that he didn't have to fear for his life.

Ash dragged the dazed Misty to the highest place in the room where Captain AJ had stood before he was vaporized. He went over the door to try and open it. Doctor Order laughed and said "It not going to be that easy to escape your doom" Misty was unresponsive.

Ash asked "Why are doing this?"

Doctor Order said "Because I am an evil soulless machine designed to do all it takes to bring Order to the chaos of everything" Doctor Order then said doubtful "I mean everything even removing uncontrollable variables permanently with violence means that I don't like doing"

"Then why do them?" Ash asked "If you don't like them"

Doctor Order said sounding unsure "I don't' know…." Doctor Order then went silent. The water reached the high point of the room.

Elsewhere, Seymour and his Techno Policemen were taken out by psychic attack from a girl with blue hair and cat like eyes from the nearby rooftop. Damian ordered "Agent Blue take out our new guest" Agent Blue moved to start climbing when a large muscular male luchador in a blue mask landed on him after jumping off the roof.

He said in a Mexican accent "No one messing with the friends of the great El Macho" and punched Damian, knocking him out. The girl with blue hair used her powers to bring the deactivated Leaf, the and the hooded female to the roof while El Macho beat up all The Techno Policemen. Seymour had fled as soon as he had recovered.

"Kat" said the hooded female "Your alive"

Kat said "Off course thanks to my new friend El Macho" They looked down to see El Macho had won and that Agent Blue and Damien had disappeared. She then said concerned "Amber, where is little Alyx?"

"I have no idea, I just following the trail of destruction" said Amber.

Kat said "I'm afraid I have bad news, It is worst then we thought I found alarming evidence that The Collector is working for Doctor Order" Amber looked distressed.

Ash was leaning on the door as the water slowly rose higher than his knees. He felt hopeless until he fell on his back looking at a happy looking Eon who was holding the door open with unnatural strength.

Ash pulled Misty out of the room and Eon let the door close. Ash said "Thanks Eon" before turning to Misty who coming back to her senses and asking "What happened? How did you get here?"

Misty said "it was all over so quick, just after you left, we distracted The Mecha-Combee. I was captured by a techno invention, A Mecha Alakazam"

Ash said "At least you okay now" Eon then motioned them to be quiet. A faint buzzing was heard just before a swarm of Mecha-Combee appeared at one end of the corridor. Everyone ran for it and Mecha-Combee Swarm chased after them.

In the control room, a hologram of The Collector was speaking with the real-life android of Doctor Order while blank looking Techno Pilots continued with their tasks. The Collector said "Fascinating The Mecha-Alakazam utilizes the power of The Moon Stone in granting it powers like a real Alakazam"

Doctor Order said "Indeed, testing of the mecha shown me it is a power source we can use to build a larger and more powerful mecha in our dream of order and perfection"

The Collector said "I should be able to replicate this power should we lose the source"

Doctor Order said "Good I have already prepared The Mecha-Alakazam's successor…."

"Wait" and The Collector said "I hear them"

Eon, Ash and Misty through ran through the endless corridors and Eon dragged them into a dark room and closed the door behind them. Mecha-Combee Swarm crashed into the door trying to get in. Doctor Order says "Surprise" as the lights turn on to show The Collector alongside two Giant Mecha-Combee bodyguards.

The Collector said "I been waiting for you" The Mecha-Alakazam, a robot Alakazam that was glowing the same color as the Moon Stone teleported into the room and trapped everyone inside energy bubbles. He said gloating "Say hello to Mecha-Alakazam, the future of robotics designed and built by Doctor Order herself" He then ordered "Bring me the Pichu" to Mecha-Alakazam. Mecha-Alakazam waved his arms and Lilly taken off Ash's shoulder. However, the little black diamond glowed causing Mecha-Alakazam to drop everyone and blast off into the wall. The Collector ordered "Get them" and the two Giant Mecha-Combee advanced. The little black diamond shot a blast of energy at two Giant Mecha-Combee destroying them.

The angry voice of Doctor Order said "You can't do anything right Victor" and a Sandshrew wearing white hi tech metal armour appeared from a chute in the ceiling. Metal Armoured Sandshrew looked mean. "Deal with them" The little black diamond shot a blast of energy but it was deflected by Metal Armoured Sandshrew's armour. Metal Armoured Sandshrew attacked Lilly with a Slash but Lilly dodged. However, it was right into the path of an energy attack from Mecha-Alakazam. Ash released Butterfree to help Lilly. Butterfree picked up Lilly just before Metal Armoured Sandshrew attacked again. Misty and Eon was just watching. Butterfree defeated Metal Armoured Sandshrew by putting it to sleep. Doctor Order then cheated by dropping in three Metal Armoured Rattata. They advance on Butterfree while Mecha-Alakazam and Lilly get locked into a battle as their energy attacks connect.

A girl with blonde hair and green eyes arrived at Porta Vista. She was horrified that Porta Vista had been turned into a massive powerhouse for Nuclear Industries with a giant metallic factory dumping green sludge into the sea from pipes. On top of this large amount of smoke came from a large smoke stack in the centre of factory. The once beautiful island had been ravaged by Nuclear Industries. The girl watched as The Techno Steamship left Porta Vista to go to Vermilion City wishing she was still on it but she had a job to do. She walked through the town and stopped where there was a pre-recorded video of a red-haired woman in a white outfit, The Director from her office within Nuclear Industries Factory. She was saying "Nuclear Industries like to remind residents that The Chairman has said that it is only harmless chemicals being dumped into the sea and that Nuclear Industries was not to blame for the high amount of toxic sludge found in the failed Techno City project" The girl was glad that she had a mission to stop Nuclear Industries from destroying nature using a secret growth herb grown in The Hidden Village.

Lilly and Mecha-Alakazam were locked in their battle with a large energy ball growing in between them. Metal Armoured Rattata were knocked out by sparks emitting from the core. Ash recalls Butterfree. Eon and Misty pull him back towards the wall as large energy ball expanded. Lilly's power suddenly boosted by the diamond overpowered Mecha-Alakazam. The large energy ball dissolved Mecha-Alakazam and a large chunk of Mecha-Vespiquen behind it.

An automatic robot voice said, "Red alert, multiple systems have failed"

Doctor Order said "Time for me to take my leave. Sorry to leave before your demise but the energy blast has forced me to retreat. Come Collector we are out of here" before it went dead and The Collector disappeared in a flash of light. Lilly glowed purple and a bubble surrounded Ash, Misty and Eon as Mecha-Vespiquen started to descend. As it descended, it broke apart and Ash caught a glimpse of a giant white Zeppelin disappearing into the clouds. it debits and deactivated drones fell on Cerulean City, damaging it. Lilly's bubble landed safely on the ground and she looked exhausted. Ash picked her up.

Misty said "Thanks for your help in stopping Doctor Order"

Ash said looking around "Even if it destroyed the city"

Misty said "The Cerulean City Resistance or what is left of it will rebuild" She searched her pockets and handed Ash, a Cascade Badge. "Here you deserved it for helping save the city" Misty forced Ash to take it before she left.

The voice of Eve made everyone jump when she said from the Pokégear-Zero "Eon, Ash, can anyone hear me, I need you help, Doctor Order has taken me to Vermilion City. Hurry" and she was silenced by a male voice saying, "Give me that"

Eon said "We have to hurry" dragging Ash by the arm.

The hologram of Chairman von Nuclear was having a meeting with a member of The Board of Executives named Joe secretly from within Joe's room inside Black Academy. Joe was a brown-haired teenager in a suit. Joe was saying "I have some information for you Chairman"

Chairman von Nuclear asked "What do have to report this time?"

Joe said "I have discovered The Collector's hired help, Isabella Black came from this academy"

Chairman von Nuclear said unamused "Is that all, I already know that Joe"

Joe said "I also discovered that Professor Technology's Daughter is here"

Chairman von Nuclear said "Really, the records say that she is in Hoenn. See if you can find out who she is and report back to me"

"Will do Chairman" said Joe switching off the hologram.


	9. Project S Part I

**Do not own Pokémon**

 **Lilly's Story: The Indigo League**

 **Chapter 9 Project S Part I**

The Director was sitting her main office within Nuclear Industries Factory at Porta Vista looking at a list of mercenaries that she had received from Chairman von Nuclear. The radio was on and it was saying "Chairman von Nuclear has taken over from Koga who has been promoted to Elite 4 status until Koga's daughter is ready to take over the gym. He assures us that he will take his duties seriously. Joining us in a few minutes is the author of Arceus is Not a God, Mr Darwin to talk about the rising threat of the religious zealots named The Church of Arceus". The Director wasn't paying attention to the radio as she was looking at the list of hired mercenaries and picking a few. The ones she picked were the fighting master named Master Chan, the 'retired' pirate named One-eyed Boris, the Kalos fashionista Madam La Fray, a mysterious man known only as The Hypnotist, a Pokémon poacher named Hunter Calvin, a so called super criminal named Captain Squirtle and Isabella Black's only equal and employee of the secretive Chaos Corporation named Pandemonium. Chairman von Nuclear wanted to use the mercenaries to help capture Project L as Professor Technology and his men were useless as well as doing a few little jobs.

Ash and Lilly were being dragged by Eon down a path that headed into another forest. They did not notice that a secret camera in a fake Pidgey sitting on a tree on the edge of the forest that picked them up. Eon suddenly stopped walking. Ash asked "What's wrong?"

Eon said "Listen, I think hear something" The faint sound of foot stomps were heard coming closer their location. A giant robotic Mecha-Cacturne came stomping out the trees. Eon said "Run!" as Mecha-Cacturne shot needles out of it hands. Eon and Ash were separated in the confusion of escaping from Mecha-Cacturne. Ash ran until he encountered a teenage girl.

She said crossly "What are you doing on Black Academy grounds" Before he could answer Mecha-Cacturne came out of the trees. The girl released a huge shiny Blastoise. Shiny Blastoise shot a blast of water at Mecha-Cacturne. Mecha-Cacturne collapsed due to the mecha not being water proof.

Ash asked "I'm Ash Ketchum and you are? and what do mean Black Academy grounds?"

The girl said while calling the Blastoise into a pokeball "I am Giselle Technology, Headmistress of Black Academy, a school created by reclusive business man. Before you ask, yes I am the daughter of the mad scientist Professor Technology"

Ash asked "So Black Academy?" to change the subject.

Giselle said "Well The Pokémon Technical Institute or now Black Academy after the reclusive billionaire took over is a boarding school which guarantees entry into the Pokémon League upon graduation"

Ash asked "Anything else I should know?"

Giselle said "Well let me see" as thought about things. She finally said "I can't think of anything. anyway, you better follow me as you don't want to get lost in this forest especially if any more of those machines are around"

Nearby Joe was spying on her from behind some trees and collecting some information on her. Seeing Project L was unexpected. He was sure that The Chairman would be interested. He moved to follow them when he was knocked to the ground by Isabella. He was picked up by Isabella to face The Collector. The Collector said sinisterly "Hello" before everything went black for Joe. The Collector said "Take this guy to Doctor Order"

Ash and Lilly are led by Giselle to an ancient grand building. She said "Welcome to Black Academy" as she led him towards an entrance under a clock tower. Ash followed her inside to see a long corridor. As Giselle led him down a corridor of pictures of past students including what appeared to be Isabella Black but labelled as Havoc. However, Ash stopped walking when he caught sight of a picture of The Collector with the looming figure of Chairman Von Nuclear with a tag saying pictured is the genius Victor von Nuclear Junior and his father Victor Senior underneath it. Giselle noticed he wasn't moving so she came back to see what he was looking at.

She said "That is our founders friend and main sponsor of the academy, Victor von Nulcear, The Chairman of Nuclear Industries and his estranged son who is also called Victor. Come we can talk more in the privacy of my office" Ash and Lilly found Giselle in the door at the end of the corridor.

Elsewhere a white Zeppelin with a black O on the side was flying over the same forest when it suddenly stopped. Inside within a very hi-tech lab, Doctor Order had placed The Moon Stone in a large device that resembled a giant metal Pokémon Egg. She pressed a few buttons on a nearby computer with a picture. The Metal Egg started to crack under the pressure of using The Moon Stone to create a Pokémon. The Metal Egg fell to pieces showing a shiny Gardevoir with eyes that glowed the same as the Moon Stone. Doctor Order said "I name you Kosma"

The Collector entered the grounds of Black Academy. The deputy headmaster, an elderly man with a moustache named Mr Harrison saw The Collector and said rather friendly "Welcome Victor, we weren't expecting you"

The Collector said "Last minute visit. Didn't want the old man knowing I was here"

Mr Harrison said with sympathy "I understand son"

The Collector said "Just here to see you and talk"

Mr Harrison said with a friendly smile "I always have time for my favourite ex-student". Mr Harrison started walking towards his office not noticing The Collector place a box with the letter S on the floor.

Inside Giselle's office, Ash was sitting on chair on one side of Giselle's desk while she sat on her chair on the other side. Giselle was saying "So as you can see, The Collector aka Victor von Nuclear was one of our best students before he became what he is today. A villain who wants to collect unique Pokémon and rare artefacts" before she started the topic that she wanted to talk about. "it not accident that we met in the forest"

"What do you mean?" Ash enquired suspiciously

"I saw you on The Academy's Pokémon cameras and knew that the pichu with you is Project L. I wanted to meet you so I can tell you what I know" said Giselle. "Project L is one of my father's projects. He wanted to use Project L to control something else that he referred to as the most powerful Pokémon ever. That all I know about Project L. If you want to ask any questions then I do my best to answer them"

Ash asked, "Why would The Collector and Doctor Order be working together?"

"No Idea" said Giselle looking worried "However what I know of Doctor Order, It is more likely Doctor Order wants her for some plan to bring Order. That was the main flaw of the AI, her obsession with Order" Some black sand came under the door of the office as Giselle was talking. "Doctor Order is completely insane and likes to pretend to be her original pre-insane self" The black sand formed into a Shiny Sandygast with red eyes. It made a horrible sound catching Ash and Giselle's attention. Giselle quickly released her Shiny Blastoise who dispatched it with water. Giselle said "We need to get out of here, I believe that was a Specimen S1, offshoots of Project S who never go far away from Project S" Giselle opened her door to see a large group of Specimen S1s heading towards them. She shut the door "Follow me" and she climbed out of her window. Ash followed her quickly. Ash follows Giselle around the building until they can see Project S, a giant Shiny Palossand with red eyes, blocking the entrance/exit of the academy. Specimen S1s were breaking off Project S. "Do you have any water Pokémon as Water is Project S's only weakness"

Ash said "No I haven't"

"Stay back here and I will deal with Project S" Giselle ordered. Ash watched as she used her Shiny Blastoise to defeat Specimen S1s and then start hitting Project S. It flinched as water hit it.

Ash is distracted by The Collector saying "Hello Again, you may of defeated my Mecha-Cacturne" Ash turned around to see The Collector on his flying machine. "But this time I afraid you will lose to Project X aka Wondertomb" The Collector threw a black ball and released a Spiritomb who was red where normally be green "Nothing can defeat him, he is invincible. Wondertomb use Shadow Ball" Wondertomb used Shadow Balls to attack Ash. This forced Ash to retreat towards Giselle and Project S who was too big for Shiny Blastoise to destroy as it reformed as fast as Shiny Blastoise water destroyed it and the specimen S1s coming off it. The Collector said "Give me the pichu and I leave peacefully"

Ash said "Never"

The Collector ordered "Project S duplicate and Wondertomb take out the Blastoise" Wondertomb's shadow ball knocked Shiny Blastoise out while Project S spat 3 globs of normal sand which turned into giant normal form Palossands with red eyes aka Specimen S2s. All four formed an iron clad ring around Giselle and Ash. The black diamond around Lilly's neck started glowing. The Collector said, "Project S destroy them" Project S and Specimen S2s used their version of Sand Tomb to bury the academy. However, Giselle, Ash and Lilly were save by Lunala. Lunala dropped them off outside of the gate as the whole academy including Project S and Specimen S2s was absorbed by black quicksand.

Lunala said to Ash and Giselle "Run" and both ran into the forest.

The Collector ordered "Wondertomb attack" Wondertomb used multiple Shadow Balls but Lunala dodged all of them while looking for a weakness. The Collector said getting tired of Shadow Ball missing "Wondertomb use Hyper Beam" Wondertomb powered up it Hyper Beam however Lunala swiftly took out Wondertomb with a Moonblast. The Collector said with disbelief "That's impossible" as he recalled Wondertomb. He watched as Lunala disappeared. He decided to withdraw back to The Order Zeppelin to report back to Doctor Order on Wondertomb's defeat. He did not notice a pair of red eyes appear in the sand.

At a secret island lab, a Doctor Fuji was overseeing Project M2's development. Project M2 was the second time that they tried to use the DNA of Mew to create the ultimate Pokémon. This time however The Aurora Virus extracted from The Birth Island Meteorite was being pumped into Project M2 and as its controller Project L had been. Doctor Fuji was against the use of the virus which created the greatest horror Project Zero which was stored within an isolated computer within Tech Manor. However, he was however too afraid to go up directly against The Chairman, Professor Technology and the man responsible for synthesising The Aurora Virus in the first place and his intermediate boss, a man named Archer.


	10. Project S Part II

**Do not own Pokémon**

 **Lilly's Story: The Indigo League**

 **Chapter** **10** **: Project S Part II**

Captain Eva and Bravo Squad were traveling inside a Mecha-Torterra, slowly moving through the forest containing Black Academy on orders of Chairman von Nuclear to find and destroy a hidden village that was suspected to home to Team Nature. Captain Eva wore a special set of prototype armor resembling The Techno Samurai but with a belt. Captain Eva was saying to Bravo Squad, men dressed as white riot police gear. "This is may be our first mission but The Chairman believes that we can succeed in our mission to eliminate Team Nature's base camp. I too believe that The Chairman's faith is not wasted" She held a look of yearning when mentioning Chairman von Nuclear.

A member of Bravo Squad said "Captain, something is happening at The Academy"

Captain Eva ordered "We Investigate, it could be Team Nature's doing"

Ash, Lilly and Giselle were wandering through the forest trying to find the path out to Vermilion City. They were fighting over who led them astray. Giselle was saying "It's all you fault, I told you to go left"

Ash said "But you also got us lost in the first place by deciding to go this way from the school" Lilly glared at him making him feel guilty for fighting with Giselle. He said joking "A benefit to being lost is The Collector won't be breathing down our necks"

Giselle said "That's true" She then said "Sorry for blaming you, I'm just taking losing the academy badly" They walk down a path for a while and decide to take a break by a river. Then both saw an Oddish with a special collar having a drink in the river so did not see Lilly walk off into the trees as she wanted to explore. She trips and bangs her head on a ground knocking herself out so did not see a Bulbasaur with the same collar of Oddish appear and use its vines to put her on his back. Giselle releases Shiny Blastoise hopping to capture Oddish so she can get a Bellossom. Shiny Blastoise easily defeat Oddish. Her Poké Ball is deflected by the appearance of The Bulbasaur before she can claim it. Bulbasaur attacks and defeats Shiny Blastoise with a powerful Razor Leaf. Ash sends out Butterfree to use a Sleep Powder attack, but the Bulbasaur blows the powder back at Butterfree. Both Oddish and Bulbasaur with Lilly run off into the underbrush. Giselle shook her head and said to herself "The Pokémon is something else"

Ash said "They got Lilly" pulling her from her thoughts. They follow run after them and attempt to cross a rope bridge, but an unnatural wind starts ripping the bridge apart. Ash and Giselle make across before it collapses. Ash however falls through the floor into a covered pit. Giselle pulls him up. A few moments later Giselle trips over a hidden vine and they find themselves suspended in a net made of vines.

Elsewhere Captain Eva and Bravo Squad have just come across the hole that used to be Black Academy with a path of destroyed trees and bits of sand leading off into the forest. A member of Bravo Squad asked "Captain, what could of done this?"

"One of Professor Technology's experiments" said Captain Eva looking shaken. She ordered "Put out an alert to All Techno Agents that one of the projects is free"

"Aye Captain" said another member of Bravo Squad.

"Now we get back to finding the hidden village and hope we don't come across it" She then ordered

"Captain? Are you sure, we are not trained in dealing with one of The Professor's experiments" said another member of Bravo Squad. Captain Eva thought about it but in the end her determination to complete The Chairman's direct order so he will think she was worthy to be with beat her fear of The Professor's experiments. She smiled as she fantasized about destroying the village and defeating the project. Then The Chairmen declaring that he knew she was strong enough to be with him. "Captain, What we doing" said the same member trying to get her attention.

Captain Eva said "We will complete The Chairman's orders, I will not let one of those experiments stop me from obeying The Chairman's commands" Her men looked at her with a concerned look but obeyed her orders.

Hours later, back in the net, Ash and Giselle were losing hope that someone would free them when a man in Team Nature uniform came along. He cut them down and said in a threatening tone "Follow me" He led them towards a large tree top village populated with Pokémon, strange green glowing herbs and a few Nature Grunts. Ash and Giselle were led to a girl dressed in a white Team Nature uniform. Ash and Giselle notice the large number of Pokémon compared to a small number of Nature Grunts in the village.

"Welcome, I am Melanie, The leader of The Hidden Village" said Melanie. She said to The Nature Grunt. "You may leave us" and he left. A girl who looked exactly like the girl with blonde hair and green eyes that was at Porta Vista came over.

She asked "Is this your Little one?" Ash saw Lilly had a bandage on her head and nodded. She handed Lilly over. "I am Spring"

Giselle asked "Do theses belong to your group Melanie"

Spring explains "This is The Hidden Village, a place for abandoned or injured Pokémon to come to rest and relax. Melanie and the others then care for them until the power of magic herbs heal them"

Melanie continues with "I collect The Herbs to use for the medicine though I'm unqualified to be a Pokémon doctor and Spring uses her power to heal the most heavily injured". Melanie then said to "This place is a place of healing so the traps are to protect these Pokémon. We only care for healing the sick and injured so if any of you have any grievances with Team Nature then please leave them outside of the village"

Ash said "I promise you Melanie that we won't capture any of the Pokémon in the village or cause any trouble" trusting Melanie.

Giselle agreed with "Only bad guys try to capture sick Pokémon anyway" Bulbasaur comes over and tries to get Ash and Giselle to leave the village.

Melanie says "Bulbasaur, They are our guests" Bulbasaur looks at them and stalks off. Melanie explains "Bulbasaur has volunteered to protect the whole village so is distrustful of new faces" They are interrupted by a massive shriek. They see a giant Project S with bits of buildings sticking out of him and made of a mixture of normal sand and black sand. It tries to devour the village with massive vacuum originating from its mouth. Melanie herds everyone out of the path of Project S's vacuum but Lilly gets caught in the suction and much to Melanie horror as well as the special growth Herbs. Bulbasaur rescues Lilly with its Vine Whip and Ash helps block the wind so it can carry Lilly out of the vacuum path. The herbs cause Project S to start to shake and start to grow. However, many different Pokemon glowing slightly green came from the surrounding forest and attacked Project S. This enabled everyone to escape the village before Project S expanded and devoured the village. Melanie asks Ash "take Bulbasaur with you. I feel that Bulbasaur will help you" Melanie and Nature Grunts alongside all Pokémon including the injured and ones that came out of the forest disappeared in flash of green. Spring however remained behind.

Spring said to Ash and Giselle "Follow me, we need to get out of the forest and get help to deal with that monster" Spring led them away from the still growing Project S who was happily devouring the village and surrounding forest. Bits of Project S were breaking off to form Specimen S1s who were Project S's original size.

Bravo Squad was going through the forest when they were contacted by a small hologram of Chairman von Nuclear. Captain Eva said "Chairman, What do you need"

The Chairman said "Zeus has detected that Project S has done your job for you. Damian will meet you near the Pokémon Center by Route 24 for further instruction" He disappeared.

Captain Eva said "You heard The Chairman, we are heading to The Pokémon Center on Route 24"

Under Pokémon Tower, the man in hooded black robes wearing a skull mask who was part of The Blood Cult from Kalos was standing in front of The Unknown Tomb which was engraved with ancient symbols of protection. He was holding an Elixir of Life made from the blood of Xerneas mixed with The Aurora Virus taken from his time from working for The Techno Institute before he met a member of Kalos Nobility named Lady Plasma. Lady Plasma opened his eyes that the world was dirty and needed to be cleansed. She told him that The Techno Institute was spreading the dirt by causing the creation of Team Nature, doing nothing to stall the spread of The Church of Arceus and The Liberation Party's quest for power. She mentioned that only the pure of blood aka the good would survive the coming Judgment Day. She entrusted him to Pokémon Tower to start the process in Kanto by awaking a supernatural monster buried within The Unknown Tomb. He broke open the tomb to see what appeared to be a decaying human corpse that look like it attempted to crawl out of the ground before it died. He did not notice a Pokémon ghost watching him.


	11. Project S Part III

**Do not own Pokémon**

 **Lilly's Story: The Indigo League**

 **Chapter 11 Project S Part III**

A newsreader was saying on Professor Oak's TV "Today's Top Story, The Techno Institute is facing legal action today for the destruction of Cerulean City and for the attack on Viridian City Pokémon Center after the technology used in these attacks were found to be theirs and illegal. These are of course the Mecha-Meowth and the gigantic Mecha-Vespiquen alongside all its drones. The Techno Institute if found guilty will have to pay for all the damages which will cripple the company financially. Others are also want them to add The Pewter Museum of Science incident to the rap sheet as people believe Isabella Black used another piece of illegal tech from them" He then paused and said urgently "This just in a giant monster that looks like a giant Shiny Palossand has been spotted in The Black Forest. More on it as it develops" Professor Oak stopped watching when he heard a knock on his door. He opened his door to see a very tried looking Gerald.

He said surprised "Gerald?"

Gerald said "Professor, I have something to tell you" before he collapsed.

Ash, Lilly and Giselle were following Spring. Spring was talking. She was saying "The trail we are following intersects Route 24, which in turn leads straight to Vermilion City where we get help to destroy that monster" Spring suddenly stopped and pushed Ash and Giselle into the shadows of trees. An army jeep, containing Damian and a couple of Nuclear Soldiers, members of The Chairman's private army, blasted past the group. After a few minutes, Spring satisfied that they are gone starts towards The Pokémon Centre. A large shadow suddenly falls across their path, causing them to look up in alarm thinking Project S had gotten in front of them. However, it is only a Charmander sitting upon a rock as having cast the shadow.

Spring said gritting her teeth "Look at how weak its tail flame so he probably needs help" Ash throws a Poké Ball at it to try and catch it so they can take it to The Pokémon Centre. The Charmander whacks it back with its tail not wanting to move.

Ash asks "Should we weaken it first?"

Giselle suggests "I try because Blastoise will help weaken him"

Spring still doesn't think it is that strong because of its small flame and suggests "Try again" Ash throws the Poké Ball again, and this time it pulls the Charmander in. However, it breaks out quickly as it is determined not to move. They are surprised by how much determination the Charmander has. Spring stands in front of the Charmander and put her hands to the Charmander head. Spring says "oh his waiting for someone on the rock for someone else to come pick him up. I hope they come soon as I can't stand to let poor Pokémon wait for their trainer" Suddenly one of Giant Specimen S1s emerged from the trees. Giselle releases Shiny Blastoise who dispatched it with ease. However more Giant Specimen S1s and normal Specimen S1s emerged from the trees. Giselle decided to retreat and dragging away a reluctant Spring who did not want to leave the Charmander. Ash followed with Lilly jumping off Ash's shoulder without him knowing. Charmander looked at her and grinned and he patted her head in thanks at waiting with him. Giant Specimen S1s and normal Specimen S1s ignored the Charmander and Lilly.

Damian in the meantime had parked the jeep next to camp of Nuclear Soldiers with a truck that had a giant pillar like machine. WM1 was written on the pillar's side which stood for Weather Machine 1. Damian looked on as one of Nuclear Soldiers turned on the device causing it to rain. He said "Good, it actually works, now we wait until Project S is weaken and we will go in and recapture it" As he was speaking Bravo Team arrived.

As it soon starts to rain, Ash, Giselle and Spring reached the Pokémon center. The rain washed Giant Specimen S1s and Specimen S1s away. As they enter Ash realizes that Lilly is gone but Giselle stops him for going back outside. She says "I am sure Lilly is around the center as she wouldn't be out in this rain would she"

Yet Lilly and Charmander was still on the rock. Charmander vainly trying to protect its tail flame from the rain with a leaf (as it will die if its flame goes out) while Lilly hugs him to keep warm. The stone around her neck glowed and protected them from the worst of the rain.

Back at the Pokémon Center, Everyone is having some soup with Spring is still worried about the Charmander. Ash says to try and cheer her up "there's no way the Charmander would have waited around that long but I am worried where Lilly is"

Giselle agrees and states "that Trainer surely would have gotten it by now" However, they hear laughter nearby, and look over to see The Collector surrounded by a group of kids listening to his every word.

They are awing over photos of his vast Pokémon collection, which is pretty sizable, when one of them asks "Have you got a Charmander too?"

The Collector reveals "I did, but I found another more unique one, I left it on a rock out in the middle of the woods promising to return for it, I had and still have no intention of doing it" He laughs cutting right though Spring. Ash and his friends realize that it must have been his Charmander they saw and then when The Collector talks the Charmander's loyalty to him confirms it. This pushes Spring over the edge; her eyes start glowing green. She stands up and storms over to The Collector. While they continue to laugh about how the Charmander is probably still waiting, this also feeds the rage that Spring is feeling.

Spring confronts The Collector, telling him in a voice showing that she was dangerous "Get the

Charmander or I will make you" The Collector did not show it but he was actually scared. He did not want to show it to his fans. So he stupidly pushes Spring who wasn't expected it so fell straight onto the ground. Spring said in a low voice "You will pay for that" She leaped at him and knocked him over. She was about to strangle him when Ash and Giselle pulled her off him. The Collector wisely fled.

Ash said "The Charmander" snapping Spring out of her rage. The three run back through the pouring rain towards the rock where the Charmander is, only to find it is now having worse problems than the weather, they saw a failing glow as Lilly was out cold. They see what seems to a starving female Eevee circling the failing glow around Charmander and Lilly. Eevee attacks when the glow goes and Charmander puts itself in front of Lilly to defend her from it. Ash tries to drive it off by throwing a rock at them, but this only causes her to move into attacking him and his friends. Spring dived at Eevee. She rolled with it. The Eevee scratched Spring but she just put her hands on to Eevee's muzzle. Her natural power boosted by her anger made a green glow around Eevee, calming Eevee right down. Ash asked, "What is this?"

Spring explained "I have the power to tame Pokémon and communicate with them" before saying with a fresh bout of rage "it seems poor Eevee was abandoned a day ago after hatching from an egg" Spring held Eevee to her chest.

Giselle said urgently "Guys we need to that theses guy to the Centre"Ash picks up Lilly who still out cold while Giselle picked up the Charmander.

They race back to the Pokémon Center and Ash asks Nurse Joy "help". Nurse Joy is angry at The Collector and is wondering how he could have let the Charmander get into such bad shape.

Nurse Joy said "He seemed a nice kid yesterday" before asking "What about the Spiky Eared Pichu?"

Giselle said "that's was our fault and we are all sorry"

Spring pleads with Nurse Joy "Save the Charmander and the Eevee" and she promises to do whatever she can. From there, there is nothing they can do but wait.

Nurse Joy soon comes out, though, and reports "The Charmander has pulled through, and it will be fine by morning but The Eevee might not"

Spring asked tone full of worry "Can I stay with the Eevee please?" Nurse Joy nodded and led Spring inside.

Inside Tech Manor, Professor Technology was once again talking with holograms of The Board of Executives led by Chairman von Nuclear which did include Seymour, The Director and a teal haired man who was Archer. Two of seats were empty where Damion and Joe sat. Professor Technology was saying "Gentlemen, what are we going to do about the crippling fines to the company"

Chairman von Nuclear said "Professor, The Board and I have agreed to that The Techno Institute will merge with Nuclear Industries with to form Nuclear-Tech Conglomerate, a larger more powerful company. We will iron out the details later but know this Professor, Project M2 will continue as previous planned. Now on to the second order of business. We still have the outstanding orders of business. Your 2 weeks has ended and we are in a worst state then before we started. Doctor Order has destroyed a valuable mecha, Team Nature is still around and Project L is still out of our hands. Fortunately, The Master Plan is still on track as Operation Pewter City was a success, Brock is out of action. We are on track as Misty is too busy dealing with rebuilding her city and I have taken over from Koga. We will move next to eliminate Lieutenant Surge and Sabrina"

Seymour asked "How are we going to get rid of them? Lieutenant Surge is a highly skill veteran and Sabrina is a powerful psychic"

The Director answered with "I have hired various mercenaries to carry out these tasks"

Chairman von Nuclear said when she has finished "One-eyed Boris will eliminate Lieutenant Surge when he goes on his trip on The Techno Steamship. Sabrina on the other hand will require a more delicate approach that I will still need to plan. Next time we will talk about an alliance with The Liberation Party and talk about ways to destroy The Blood Cult sect forming in Johto and Kanto. Meeting adjourned" The Board of Executives then vanished. Professor Technology went over to his computer to finish his plan to remove The Board of Executives especially if Nuclear-Tech Conglomerate merge happens. The merge meant he did not have the time he thought he had.

later that evening, Damion looked pleased as Weather Machine 1 preformed as expected when he turned it off. Project S would be recaptured with ease. He turned to Captain Eva. He said "I have it under control it Captain, The Chairman instead want you to capture Project L as it is nearby while I finish with dealing with Project S"

Captain Eva said "I do as The Chairman orders" and she and Bravo Team left. Damion went over to his jeep to get himself something to eat and report to Chairman von Nuclear. As He reached the jeep, Project S came crashing out of the trees. Project S just looked like a giant mound of sand after the rain. Damion said to The Nuclear Soldiers. "It is time" Weather Machine 1 transformed into Mecha-Castform 1.0, a giant robot Castform. Damion's plan was coming along as he planned despite Project S being larger then he remembered.

When morning came, Ash awoke to Spring shouting "Charmander has disappeared from the ER room"

Ash says while rubbing his eyes "I'm certain that the Charmander has simply gone back to the rock"

Spring says "I want to go after it again, just to know that Charmander ok"

Giselle replied as appeared "It will be no use., the Charmander is loyal to The Collector, and nothing is likely to change that. We can't force Charmander to go with us if it doesn't want to" Spring looked conflicted so Giselle added "We still need to wait on the Eevee" Spring looks disappointed.

Ash points out "Charmander knew we cared about it, but he couldn't forget about Damian"

Giselle says "We should go for a walk while we wait"

Nearby Team Bravo was waiting outside of Pokémon Center, grouped around their newest mecha,

Mecha-Onix, a larger robotic version of an Onix as Captain Eva did not want to Mecha-Torterra to be damage if they fail. Captain Eva said "This is the future gentlemen, once The Chairman's Master plan is competed then we be unstoppable"

One Bravo Member asked "What About Team Nature?"

Another one said "Don't forget Doctor Order"

Captain Eva declares "Machines will defeat nature. Besides soon we will no longer need pokemon and Doctor Order is prime example of an excellent machine" as she climbs into the mecha. "We have a job to do gentlemen. Suddenly Captain Eva sees Ash, Lilly, Spring and Giselle walking along so says "Main target sighted, is the trap is set…" She waited for a response "good" Bravo Team quickly hide. Ash and Spring trigger a pitfall. They fall into the hole. Giselle was a few steps behind as she seen one of Bravo Team hiding behind a tree. The Bravo Team and Mecha-Onix then appear. A member of Bravo Team easily pulls Lilly from the hole. He backs away after putting Lilly to sleep. Ash realizes that they are in trouble. So he quickly tries to climb out of the pit, but fails. He tries to get Spring to help him escape but find that they can't reach the top. Giselle was grabbed before she could do anything.

Captain Eva said via a robotic voice of Mecha-Onix "Well that wasn't that hard was it didn't know what the others problem were" Mecha-Onix turn to leave, but at that moment Charmander steps in their way.

Charmander, as translated by Mecha-Onix orders them "Give her back"

Captain Eva naturally refuse and warns "Beat it weakling or else" Charmander responds by closing its eyes, focusing hard, and unleashing a massive Flamethrower, which roasts quite a few members of Bravo Team. All of them fled from this show of power. Captain Eva said "Now you done it" She pressed buttons and a laser shot at Charmander. Lilly jumped in front of the laser and The little black diamond defected it back. The laser destroyed the Mecha-Onix and Captain Eva went flying off faraway. The Collector who was following Ash and Lilly shows himself after seeing Charmander was powerful. Giselle helps Ash and Spring out of the pit.

While The Collector walks towards Charmander with a happy grin, Ash asks Charmander "Do you want to come along with us"

However, The Collector says "I have come back for you just as I promised"

Ash says barely containing his anger "You were just bragging about how you abandoned Charmander" The were interrupted by the looming figure of Project S. The Collector instantly looked more confident.

Damian was running through the forest as his plan had fell apart. Mecha-Castform 1.0 had failed to defeat what remained of Project S and had been destroyed. Damian pulled out a phone to contract The Chairman. He however froze when he felt an unnatural coldness. He saw Winter who was smirking and eyes gone white like ice.

Winter said with a sadistic grin "Well look who we have here, Little Damian" Nature Grunts appeared, all had glowing green eyes. Damian was afraid that Winter was one running Team Nature after all.

Also at an abandoned lighthouse, a man named Bill was had converted into it to his living space as he was hiding out there. Bill was an ex-employee of The Techno Institute. He was listening to the radio to gain knowledge on current events. A man was saying "The Techno Institute has been found guilty of creating illegal technology and for creating the monster currently attacking Kanto after a parcel containing evidence of its creation appeared at court. Witnesses say they saw a Shiny Gardevoir with glowing eyesdrop it off. What this means for The Techno Institute we will find out in the coming days. Coming up next, Mr Darwin is back and this time to talk about his new book, The Evolution of The World: From Mew to Man"

Bill switch the radio to another station and a woman was saying "The Weather patterns have once again point to signs of another Super Storm hitting Kanto in the future. Many of us would remember that The Super Storm, whose center was over Cinnabar Island, caused destruction on a large scale across Kanto leading to The Techno Institute rebuilding Kanto when the storm broke up. Tune in tomorrow when we talk to President Harmonia, Head of The Liberation Party about the claims that President Harmonia rigged the Unova election to make sure that he won" Bill turned off the radio and he was concerned. Bill knew a lot from his time working at The Techno Institute and much of it was stuff that Professor Technology wanted to keep a secret. His knowledge meant he was worried on the events to come. He heard a knock on his door. He said cautiously "Who is it?"

A tried female voice said desperately "I am Eve and I just escaped from a goon working for Doctor Order. I need sanctuary. He is tracking me as we speak" He didn't hesitate however to open the door and let the girl inside. He said "So why did Doctor Order want you for?" as he turned he back to make a hot drink.

Eve said "Oh she wanted to set up a trap to capture Project L" putting her hand in her pocket.

"How did you escape her" asked Bill astonished that someone escaped that insane AI's plans. He did

not see Eve pull out The Genesis Gun.

"Oh, it was easy really" she said "When it is your trap and plan" before Bill could do anything with the revelation that Doctor Order had tricked him. She shot him with the Genesis Gun. She was saying as his world started to go dark. "It be interesting to see what will happen but Lieutenant Surge and I have something pressing to do so I am afraid what will happen personally. See you later Bill" Bill last thought as he fell unconscious is that he couldn't believe that Lieutenant Surge was an agent of Doctor Order.


	12. Project S Part IV

**Do not own Pokémon**

 **Lilly's Story: The Indigo League**

 **Chapter 11 Project S Part IV**

Captain Squirtle, A man dressed in an outfit resembling a Squirtle alongside wearing sunglasses was in an underground network of caves with his army of Squirtles who were also wearing sunglasses. Captain Squirtle was talking to Isabella's friend C on a video screen. He said to his employer "I see you sold my contract to The Chairman"

C said "I personally recommended you to my buddy Victor Senior"

Captain Squirtle asked "What shall I do?" which had a hidden meaning that only C would know.

C said "Just do as Victor Senior has commanded and destroy Project S" Captain Squirtle knew then that C was ok with The Chairman's plans so he did not need to do anything extra.

Giselle, Ash, Lilly, Charmander and Spring were slowly backing away from Project S while The Collector walked forward towards Project S. Project S lifted him up on top of it. He ordered "Attack them" Project S moved forward.

Giselle released Blastoise and said "Run I hold them off" Ash did not want to leave her but Spring decided to retreat to prevent Lilly from being taken by The Collector. They ran through the trees and fall into a pit. The Squirtles wearing sunglasses peer into the hole. The Boss Squirtle sees Lilly and smiles with smirk. The rest of them start laughing. They then all disappeared from Ash's view. He did hear a battle of some kind.

He suddenly hears The Collector yelling "Damn it" before silence. An Officer Jenny and Giselle soon pull them out of the hole. Ash sees the washed up remains of Project S lying nearby and puddles of water. The Collector and The Squirtles were nowhere in sight. Officer Jenny then takes them to the police station in a nearby town.

At the police station, Giselle explains what happened "Project S has been defeated at last. Blastoise and a group of Squirtles dealt with it. Officer Jenny arrived on the screen just as Project S was destroyed"

Officer Jenny added "Those Squirtles belong to Squirtle Squad, a group of Squirtle that have all been abandoned by their Trainers and are now controlled by a super villain named Captain Squirtle. They been terrorizing the area for a week now. They also seem to have taken The Collector captive. It would be helpful if you help me get both The Collector and Captain Squirtle into custardy"

Giselle said "We should help as It is a chance to get The Collector off your back"

Officer Jenny said "We believe that Captain Squirtle is hiding in the nearby forest"

A short distance away, The Collector stunned from crashing into the ground realizes that the Squirtle Squad had surrounded him. Captain Squirtle tells him coming out of the shadows "Well look here. It is The Chairman's brat of a son" He menacingly "Your father will probably want to see you" He orders his Squrtles "Take him"

As this was happening Professor Oak was watching TV in his lab waiting for Gerald to wake up. He was watching a program titled True Crime: The Story of Father Roy which was an old program about the founder and leader of The Church of Arceus. A narrator was saying "Father Roy was religious nut job that used to work The Techno Institute. He was fired by Professor Technology when he started claiming that The Techno Institute had been playing Arceus and creating life. Join us after the break where we have interviews from the author Mr Darwin, Director Ariana of Nuclear Industries and his ex-work colleague Winter Frost about their views on Father Roy" as the break was occurring Professor Oak was thinking of what Gerald told him about the androids that attacked him and the disappearance of Zana. He knew of only one man that had the capabilities to build such realistic androids. Professor Oak then heard a knock on his door. He opened the door to see a woman with silvery-blue hair and eyes. She wore a white outfit like The Director or Ariana wore.

"Hello Professor" the woman said "I am Karen and I am here to invite you to be a judge at The Nuclear-Tech Conglomerate's Beauty Contest at Porta Vista where you will judge alongside Lady Plasma and Mr Darwin"

"Nuclear-Tech Conglomerate?" The Professor asked.

"You haven't heard" Karen said "The merge of Nuclear Industries and The Techno Institute has gone through. This contest will be our first event and the celebration of the event. So will you be a judge?" She asked.

"I suppose so" Professor Oak answered.

"We be around to pick you and anyone you want to come will you in a couple of days" Karen said. Professor Oak watched as Karen left. He decided to go and check on Gerald. Gerald was however still out cold so he went back to what he was doing.

Ash, Lilly, Giselle and Spring were resting after walking through the forest looking for Captain Squirtle's Lair. Spring and Ash were sitting and talking while Giselle fished in the nearby river. Officer Jenny remained at the station just in case Captain Squirtle surfaced in town. Lilly was next to Ash asleep. They were there as they had found what appeared to a ruined Nuclear Industries factory had looked like it had been destroyed by ice. After resting they would explore the ruins of the factory as they had not leads on Captain Squirtle's Lair.

Ash asked "Spring?" as he noticed Spring was staring intently at the black diamond around Lilly's neck.

Spring said "Yes"

Ash asked "Why are you staring at the diamond around Lilly's neck"

Spring looked around and said "This Diamond feels unnatural somehow. Almost like…." She trailed off.

"Like?"

"The so-called Omega Stones of which were supposedly created by a man named Omega. I say supposedly as I don't even know if Omega even existed. However, his so-called apprentice used Omega Stones to made himself very powerful"

"What exactly are Omega Stones" Ash questioned.

Spring said after looking at the river in thought "I only seen one Omega Stone, used by a vile man to enslave mother to his will. Thankfully it was later destroyed by ironically by Doctor Order in her escape. I believe that The Professor wanted to use them to powerup an abomination of a Pokémon" Spring tailed off as she remembered something else.

Ash then said "What…." but one of the Squirtle Squad members interrupting them by soaking them with a Water Gun. Boss Squirtle takes advantage of their attention on the other Squirtle steals Lilly. Ash and co chase Boss Squirtle to a forest clearing. However, they soon find themselves surrounded by a legion of Squirtles. Boss Squirtle was holding Lilly who was still asleep much to the shock of everyone. Captain Squirtle walked into the clearing.

He says "Well it is my lucky day, not only will The Chairman get his son but also Project L back" Boss Squirtle looked like he was grinning and gave a slight nod to his brothers. "Love to stay and chat but I have places to be" He and Boss Squirtle left the scene.

Elsewhere Winter was unknowingly standing over Captain Squirtle's Lair with an evil grin on his face. He was holding with a broken Omega Stone, a cracked and chipped black stone with an Omega symbol on it in hands. He was glad that he found the stone as it allowed him to keep feeding Nature anger until she causes a Super Storm. He was hoping that the Super Storm would destroy all technology. However, he would still need to test the stones power once again and The Techno Steamship will give him an opportunity to reacquire himself with harnessing Omega's power. Melanie appearance caused him to hide the Omega Stone. He put on a charming smile before speaking to her.

The Squirtle Squad retreated a few moments after Captain Squirtle left. Ash intermediately followed the direction he went to. He kept pushing forward until he hit a cave entrance. He was about to walk right in when Giselle stopped him. "Ash we need a plan, if that is Captain Squirtle's Lair then it will no doubt be crawling with Spuirtles" She realized that Ash already entered the cave with listening to her. Giselle and Spring both entered not wanting to leave Ash on his own. They unknowingly went off into a different direction.

Ash on the other hand was trapped in a net. Members of The Squirtle Squad appeared and surrounded them. The Squirtle Squad led their prisoners deeper into the cave network. Down they went until they came out into a central cave. It was full of Spuirtles, Boss Squirtle was missing however. Captain Squirtle came towards him looking confused why Ash was not giving up.

"Why are you following me when it is clear you won't win against me when I have an army at my beck and call" said Captain Squirtle arrogantly. "You can't take all of us on"

"I can do my best to" Ash said determined "I will get Lilly back"

"It will be foolish as you will not win against superior numbers"

A childlike voice said "Numbers mean nothing when help arrives" Kosma appeared in-between

Captain Squirtle and Ash.

Captain Squirtle ordered "Attack" and the Squirtle Squad all attacked. Their attack was blocked by Kosma and directly back at them. The Squirtle Squad were knocked out. Captain Squirtle was backing away in fear when Kosma implemented a psychic command to make him fall asleep.

She said to Ash "Mother thought you would have saved your friend Eve by now" Ash looked guilty as he had forgotten about Eve in the commotion with Project S. "She is feeling generous so she is giving you a chance to save Eve" She made a map appear. "Follow the map and you will find Eve" Ash found himself in a room with Boss Squirtle who was holding amazingly still sleeping Lilly in his arms. Boss Squirtle saw Ash and fled the room after placing Lilly on the ground. Ash picked her up glad she was fine. He followed where Boss Squirtle went to find himself exiting a secret door in the wall to where Captain Squirtle and The Squirtle Squad were. Spring and Giselle had caught up to him. Ash noted the strange shiny Gardevoir had vanished.

Giselle told them "I will stay here for Officer Jenny so at least Captain Squirtle will be apprehended and then I will rebuild Black Academy"

Ash said "Goodbye Giselle, I hope we met again" and hugged her. Spring waved goodbye. Spring followed Ash as he followed the map with was pointing him to a location titled The Lighthouse at Dragonite Point.

As these events were happening, Amber, Leaf and El Macho were following Kat who was using her psychic powers to track Lilly's location. They were heading in the direction of Vermilion City. Kat was asking Amber "So where did you find this android?"

Amber replied with "Laying on the ground in Viridian Forest, looks like Winter and his cronies took her out"

"At least Winter will soon keep The Techno Institute too busy from looking for us" said Kat very sure of her statements. "He doesn't tend to remain in the shadows for too long" They continue to walk in silence.

El Macho broke the silence with "Wait I can hear something" and he stopped walking.

Kat suddenly said urgently "Everyone Move" as she sensed something. The warning came too late as the ground shook and a giant Mecha-Nincada busted out of the ground knocking El Macho out cold.

Isabella's voice said coming from Mecha-Nincada "Hello princess and friends"


	13. The Lighthouse at Dragonite Point

**Do not own Pokémon**

 **UPDATE 2 [11/09/2017]:**

 **Spelling and Grammar Fixed**

 **Lilly's Story: The Indigo League**

 **Chapter 13: The Lighthouse at Dragonite Point**

Officer Jenny of Lavender Town was investigating Pokémon Tower after a minor Earthquake occurred in that location. She was just checking to see if had been damaged on behalf of Nuclear-Tech Conglomerate. She also kept an eye out for the Blood Cultist that was seen hanging around. Ominous dark clouds hung over the tower. Officer Jenny felt a chill in the air as she approached the tower. A dark evil laugh made her stop and turn to leave. An expert can deal with it she thought to herself. The same ghost who watched the cultist watched sadly as the policewoman was dragged into the ground. She will have the same fate as the cultist. The ghost was powerless to fight the creature that the ghosts had named Buried Alive since the powerful being had been buried alive under the tower by his partner.

Ash, Lilly and Spring having exited Captain Squirtle's Lair were following the map Ash received from the strange shiny Gardevoir. Spring was asking questions on the Gardevoir. Ash couldn't answer any of them. He did tell her about Eve and her being taken by Doctor Order. Spring said in response "Doctor Order is not a foe to trifled with" As they walked through the forest, Spring continued talking "We may be heading right into a trap" She enquired "So how do you want to play it?"

Ash said, "We just spring it and deal with it if it comes up" They walk onto the beach and see a beautiful sunset. Ash then sees a distant object in shape of a lighthouse when as the sunlight fades. They head towards it.

Elsewhere within a secret lab at Porta Vista, the hologram of The Chairman, an ugly woman named Captain Brutella and a woman named Doctor Nyx were standing in front of a Metal Egg plugged into four machines injecting the Aurora Virus into an egg within Metal Egg. The Chairman said, "Excellent work Doctor Nyx"

"Nemesis is coming nicely," said Doctor Nyx with psychotic glee "He should be ready before The Beauty Contest is over"

"That is good to hear as Project M2 has suffered several setbacks and I believe Doctor Fuji is deliberately stalling progress. Once Nemesis is complete, you will go to over the main lab and take over from Doctor Fuji. Archer will be expecting you" Chairman von Nuclear turned to Captain Brutella and he ordered "Organize a task force and search for a member of Team Nature that we believe to be up to something at Porta Vista"

Ash, Lilly, Spring made it to the old lighthouse, that looked like it was falling apart, just as night fell. The long walk has made them exhausted. Ash rings the bell, only to be greeted by silence. The old door swung open by itself. Ash poked his head and found there was no one there to greet him. He and Spring entered the lighthouse. They soon find themselves in a room with Bill tied to a chair and gagged. Ash soon helped him out. The first thing he said was "it's a trap" A screen came down with the shadowy figure of Doctor Order.

Doctor Order said "Welcome to my trap. Eve is in another location I'm afraid. However, an old friend of mine Mister Drake is waiting for you. If you defeat Mister Drake in a one on one fight then You can ask Bill here any question you want for five minutes. You will find him to be useful in gaining knowledge. However, if Mister Drake wins then Lilly and Eve are mine forever" She asked, "Do we have a deal or will you turn and leave?"

Ash said, "We have a deal"

"Excellent" Doctor Order said, "Let me wake him up" A strange noise was heard. Doctor Order's screen switched to the ocean. A large figure appears, rising from the ocean. It is revealed to be the outline of a giant Dragonite with red eyes. Mister Drake was taller than the Lighthouse. Mister Drake ripped off the top of the lighthouse. He towered over everyone. Doctor Order reappeared on her screen. "Say hello to why this location is called The Lighthouse of Dragonite Point, Mister Drake" Mister Drake roared. "Chose your champion" Ash looked through his Pokémon; Lilly, Butterfree, Pidgeotto and Bulbasaur and didn't know who to choose.

As this was happening Amber, Leaf and Kat were facing off against Isabella and a giant Mecha-Nincada while El Macho was out cold. Isabella's voice said coming from Mecha-Nincada "You will not be able to beat me so come with me willingly" Kat was not scared.

Kat said back "Your mechas don't scare me" as her hands lit up with purple energy. Mecha-Nincada powered up a Solar Beam. Kat got into a fighting stance. Mecha-Nincada shot its Solar Beam and Kat tried to deflect it. She struggled but in the end managed to deflect. Mecha-Nincada powered up another Solar Beam. Kat knew she did not have the energy to deflect another so went on the offensive. She shot off a couple of energy balls. Mecha-Nincada proved to have a low defence as it intermediately deactivated as it absorbed the energy. Much to their surprise, Isabella was unfazed by this setback.

She uttered "I told you that you can't beat me" as a Mecha-Ninjask burst out of the Mecha-Nincada. It used its own version of Double Team to replicate itself into Mecha-Nincada Replicas. They moved positions so Kat lost the location of the real one and then went on to form a ring around them. "Your move"

"I chose Lilly" Ash said. He was forced to use Lilly as the others were not suitable to fight Mister Drake. Lilly stood ready to fight.

Doctor Order said, "As you wish" Doctor Order's voice boomed "In one corner all the way from Birth Island we have Mister Drake. In the other corner, we have the adorable powerhouse, Lilly" Doctor Order then said slowly "3…2…1…Fight!". Mister Drake powered up a Hyper Beam

Ash ordered "Disarming Voice" Lilly used Disarming Voice and anticlimactically Mister Drake fell into back into the sea defeated. Everyone including Doctor Order was stunned at how easy Mister Drake went down.

Doctor Order recollected herself and said "I will still honour our deal. You have five minutes" Her screen shown a countdown clock. Bill tried saying something but he coughed.

Ash asked, "Do you know Lilly"

Bill explained examining Lilly "Lilly or Project L is one of The Professor's dark experiments. She was made to control a Pokémon known as Project M2"

"M2?" Spring enquired with her eyes narrowing.

"All I know is Project M2 is a manmade Pokémon" Bill answered. He then continued speaking "Using something named the Aurora Virus on her gave Lilly psychic like powers at cost of her electrical abilities"

"Have you any idea on this strange diamond around her neck?"

Bill had a closer look at the diamond, he said "I think that is a rare Alpha Diamond. I am not sure as I only seen limited information on it. They are linked to Omega Stones if I have correctly"

Spring asked wanting to know desperately "Any more information on Aurora Virus"

"It originated from The Birth Island Meteorite and its effects are unpredictable as it created a living sand monster in Project S, a very parasitic fungus in Project V and a near invincible Project Z"

"It's alien" Ash stated.

"It does come from space" Bill confirming Ash statement. Bill then disappeared before their eyes.

"That was five…well five and half minutes," Doctor Order said reappearing on the screen. "Well done making this far. If you do want Eve then you will have to defeat my lackey Lieutenant Surge, the Gym Leader of Vermilion City's Gym. See you there" The screen went black.

Spring said, "I won't be able to go with you and help as I have check on the sick Eevee"

Ash said, "I hope we meet again" Spring and he shook hands and Spring headed back to The Pokémon Centre while Ash went on to Vermilion City to save Eve and get his badge.

Captain Squirtle meanwhile was sitting in a cell alone after being interrogated. He surprised when C's Apprentice, a beautiful woman named Pandemonium enter his cell. She said, "Follow me" Captain Squirtle followed Pandemonium out of the police station where everyone was asleep. Pandemonium headed over to a creepy looking man with a pocket watch and car. Captain Squirtle as he walked decided he must shed Captain Squirtle and evolve into the stronger Corporal Wartortle.


	14. Lilly Vs Giga-Raichu

**Do not own Pokémon**

 **Lilly's Story: The Indigo Chapter Part 1 [Formerly Lilly's Story: The Indigo League]**

 **Chapter 14: Lilly Vs Giga-Raichu**

Onboard Zeus, Captain Zed had picked up on the emergence and quick defeat of Mister Drake. He was surprised The Birth Island Meteorite had caused a normal Dragonite to mutate. Captain Zed contacted Bravo Team to capture Mister Drake for further study on the effects of the Aurora Virus on normal Pokémon.

Ash and Lilly were on route to Vermilion City to save Eve and get his badge from Lieutenant Surge when they encountered The Collector and a Mecha-Meowth with 2.0 on it. This one was smaller than the original Mecha-Meowth. The Collector said via Mecha-Meowth 2.0 "Now, you can give me Lilly peacefully or get destroyed by Lieutenant Surge"

Ash said "No" without thinking as he was determined to defeat Lieutenant Surge and save Eve.

"Fine, have it your way," He said. Mecha-Meowth 2.0 advanced and then retreated. He said as he was leaving "Psyche, Doctor Order ordered me to let Lieutenant Surge deal with you" He disappeared into the trees. Ash and Lilly continued walking. They then encountered a young girl with glasses of around six covered in dirt and mud sitting on a log crying.

"Hello?" She asked with an obvious French accent after hearing him approach "Anyone there?"

Ash said gently "Hey, What's the matter?" The girl turned her teary eyes to him.

"I am lost, please can you help me find my caretaker in Vermilion City?" asked the girl. Ash glanced around and saw no one.

He enquired "What happened?"

The girl said, "My caretaker and I were attacked by Team Nature"

Ash said, "You can come with me and we see if we can find your caretaker"

The girl hugged him and said excitedly "Thanks, mister" She held his hand. "I'm Bella".

They soon made it to Vermilion City. First things first they head to Pokémon Center to get Bella cleaned up. As Bella cleaned up, the doors open and a Chansey and a Trainer run in. On a roller table pushed by the Chansey is a badly beaten-up Rattata. The Nurse Joy commented to himself "This is the fifteenth one that month"

Ash went over to Nurse Joy and asked: "What happened?"

Nurse Joy said, "Lieutenant Surge" She led Ash into a room where there are many badly injured Pokémon, including a Caterpie, an Oddish, a Sandshrew, and the previously seen Rattata. Lilly gets distressed seeing so many injured Pokémon. She put her ears in front of her eyes and snuggled closer to Ash. Nurse Joy explains "They have all been obliterated by Lieutenant Surge, the new Vermilion City Gym Leader after he disposed of the last one" Ash is starting to get worried that this Lieutenant Surge must be a powerful Trainer. Lilly seeing that he is distressed licks his ear to try and cheer him up. "He runs the city in an iron grip. He has a powerful Raichu that he uses to enforce his will"

Ash tells her "that it's time to go take on the Gym"

Nurse Joy said, "Good luck, I hope you can succeed where others have failed" Suddenly; another Trainer with an injured Pidgey comes in forcing Nurse Joy to deal with them. Ash knew he had to step up his game to get his third badge and save Eve. As he waited for Bella to come back, Ash prepared himself mentally to fight Lieutenant Surge. Bella came back looking much cleaner and in new clothes. Soon enough, they ended up outside the Gym. A picture of a giant Raichu standing over a pile of defeated Pokémon titled Dare you fight Giga-Raichu on either side of the door. That shattered Ash's confidence. He, Lilly and Bella stepped inside the gym.

Elsewhere, Eon was inside the Pokémon Center in the forest after escaping from Mecha-Cacturne watching a tv in a room she had rented. A man was saying "Nuclear-Tech Conglomerate has put Pewter City and Cerulean City under martial law with the Gym Leaders being injury or are rebuilding. The Chairman has assured us that nothing will change" Eon turned it over to another channel which was showing a woman standing in front of a theme park entrance saying The World of The Future.

The woman said cheerfully "Hi, I am Miss Penny. Here to tell about The World of The Future. A brand-new theme park coming soon to Redor Island. Book now for a week for the price of five in The Future Hotel, a six-star hotel on site" Eon rolled her eyes at Doctor Order's latest scheme.

Ash, Lilly, and Bella enter the main part of the gym, a gladiator arena where Lieutenant Surge was sitting on a chair overseeing the arena. Eve or unknowingly to him Doctor Order was chained next to him with her mouth covered. A giant gate stood underneath him. Lieutenant Surge's voice boomed "Who dares challenge Giga-Raichu"

Ash declares "I intend to battle Giga-Raichu for Eve and the Thunder Badge" Lieutenant Surge smirked evilly.

He said "Another victim for the Emergency Room. Doctor Order has ordered me to destroy you" He called out and the gate opened. Giga-Raichu, a gigantic Raichu that would look like a normal Raichu if compared to the height of Mister Drake, came stomping out. "Let's go" Ash started with Butterfree and Bella cheered him on. Butterfree was easily taken down by Giga-Raichu. Ash released Pidgeotto who went just as quick as Butterfree. Ash released Bulbasaur. Bulbasaur gave Giga-Raichu a small fight. However, Giga-Raichu took him out as well. He said laughing "The little baby brought a little baby Pokémon to fight Giga-Raichu" as Ash sent in Lilly. He laughs again and claims "A Baby Pokémon will not take down a final evolution"

Ash counters saying, "There's more to Pokémon than forcing evolution and I like Lilly the way she is" Lilly looks determined to win.

Lieutenant Surge said with a smile "I'm going to show that fighting with the big boys can be a shocking experience" Lilly is hit by Thunderbolt sent by Giga-Raichu. Lilly was hurt badly.

Ash orders Lilly "return" as she was barely standing. She refused and charged in once more.

Lieutenant Surge orders Giga-Raichu "Mega Punch" immediately followed by "Mega Kick" hitting Lilly hard.

Outside, The Collector was watching Giga-Raichu out match Lilly on a screen inside Mecha-Meowth 2.0. He begins to worry that if Lily is getting beat up like this, then he won't get Giga-Raichu, as well as all Doctor Order's scheming, will have been in vain. He pulled out an Omega Stone fragment, which fitted into Winter's Omega Stone, that Doctor Order gave him just in case Lilly's loses.

Back inside Lieutenant Surge orders the big finale and Giga-Raichu complies instantly, unleashing a powerful ThunderShock that gives Lilly the shock of her life. Lilly was on the brink of defeat when The Collector uses the Omega Stone fragment to reenergize her. The Alpha Diamond around Lilly's neck started glowing and caused the Omega Stone fragment to burn. The Collector dropped it and it caused the mech to explode and The Collector to go flying. Lilly was dodging Giga-Raichu as Lilly gained a speed boost. Lieutenant Surge looked annoyed when Lilly kept dodging Giga-Raichu's attacks. Ash said, "Disarming Voice" Her attack hit but Giga-Raichu was barely damaged. Lilly and Giga-Raichu stood face to face. Both wanting to win.

Chairman von Nuclear was overseeing the extraction of the fossil of an ancient Tyranitar, the size of Mister Drake, named Arceuszilla from the site where his main project, Nuclear Power was going to be built outside of Fuchsia City. He was disturbed by the hologram of Doctor Nyx. Doctor Nyx looked excited as she said, "Nemesis has been completed"

"That's fast," said The Chairman skeptical.

"It is amazing, the virus has bonded to the egg much like Project L and Venomothra"

"Excellent work Doctor Nyx," said Chairman von Nuclear with a smile. "With Nemesis, Project M2 and The Ancient Titans at my command, we will be unstoppable"

Back in the gym, Lieutenant Surge orders "Body Slam" which Giga-Raichu does, dropping all its weight on Lilly. Lilly manages to lift Giga-Raichu off her. Lieutenant Surge orders "Body Slam" again, but this time, Lily jumps out of the way, and Giga-Raichu damages itself. Repeated Body Slam attempts from Giga-Raichu all miss completely as Lilly became too fast to hit. Lieutenant Surge growing aggravated, orders Giga-Raichu "unleash Giga-Thunderbolt". Giga-Raichu unleashes its strongest attack. Giga-Thunderbolt hit Lilly dead on and caused the floor to be destroyed. When the smoke cleared where Lilly with her eyes glowing purple was still standing. "Giga-Thunderbolt again" Giga-Raichu unleashes its strongest attack again but this time, Lilly deflected it back and Giga-Raichu was defeated. Lieutenant Surge was also hit and he suddenly exploded into a mess of wires and machine parts to Ash's surprise. He quickly went over to Eve and freed her. Lilly came bounding over.

Eve said, "Thanks for saving me from Surge and his Giga-Raichu" She then said, "We better get out of here…." She noticed Bella and said with a happy smile and friendly voice "Hello Bella"

Bella said hugging an uncomfortable Eve with affection in her eyes "Evelyn, I'm so happy to see you" Eve holds Bella's hand. Ash picks up a tired looking Lilly.

He said, "Well done, I am proud of you" Eve came over with Bella still attached to her hand.

She handed him the Thunder Badge and said, "This for you, you defeated the gym leader Surge" Ash took the badge and wondered if any of the badges he gets were going to be a normal battle. They leave the gym just as The Techno Steamship arrives at the port.

Kat was surrounded by Mecha-Ninjask and Mecha-Ninjask Replicas. Amber and Leaf dragged the unconscious El Macho out of harm's way. Kat threw energy balls and hit only Mecha-Ninjask Replicas who were defeated in one shot. Kat was tired and the fight was taking everything from her. She did one last-ditch attempt to defeat Isabella and Mecha-Ninjask. She used all her energy to engulf all the Mecha-Ninjask Replicas, Destroying them. Unfortunately, Mecha-Ninjask remained standing and she did not notice the wreck of Mecha-Ninjask form into a Mecha-Shedinja. She did hear Isabella say, "Bad luck" as Mecha-Ninjask powered another Solar Beam and Kat collapsed onto the ground. Mecha-Shedinja then advanced on Amber, Leaf and the unconscious El Macho.


End file.
